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11 pages, 1933 KiB

Open AccessCommunication

The Influence of the Omicron Variant on RNA Extraction and RT-qPCR Detection of SARS-CoV-2 in a Laboratory in Brazil

by Lívia Mara Silva, Lorena Rodrigues Riani, Juliana Brovini Leite, Jessica Mara de Assis Chagas, Laura Silva Fernandes, Romário Costa Fochat, Carmen Gomide Pinto Perches, Thiago César Nascimento, Lauren Hubert Jaeger, Marcelo Silva Silvério, Olavo dos Santos Pereira-Júnior and Frederico Pittella

Viruses 2023, 15(8), 1690; https://doi.org/10.3390/v15081690 - 4 Aug 2023

Viewed by 1608

Abstract

The emergence of SARS-CoV-2 variants can affect their detection via RT-qPCR. The Omicron variant has a greater affinity for the upper respiratory system and causes clinical conditions similar to bronchitis, as opposed to the pneumonitis-like conditions caused by other SARS-CoV-2 variants. This characteristic [...] Read more.

The emergence of SARS-CoV-2 variants can affect their detection via RT-qPCR. The Omicron variant has a greater affinity for the upper respiratory system and causes clinical conditions similar to bronchitis, as opposed to the pneumonitis-like conditions caused by other SARS-CoV-2 variants. This characteristic increases the viscosity of clinical samples collected for diagnosis. Coinciding with the arrival of the Omicron variant, we observed a failure in control gene expression in our laboratory. In this report, we have optimized a rapid nucleic acid extraction step to restore gene expression and detect the presence of the SARS-CoV-2 virus. We reevaluated 3000 samples, compared variant types occurring in different time periods, and confirmed that the presence of the Omicron variant was responsible for changes observed in the characteristics of these clinical samples. For samples with large amounts of mucus, such as those containing the Omicron variant, a modification to the nucleic acid extraction step was sufficient to restore the quality of RT-qPCR results. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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13 pages, 1644 KiB

Open AccessArticle

A Comprehensive Phylogenetic Analysis of SARS-CoV-2: Utilizing a Novel and Convenient In-House RT-PCR Method for Characterization without Virus Culture and BSL-3 Facilities

by Yen-Ju Chen, Jason C. Huang, Ching-Ping Yang, Kuo-Feng Hsu and Hsin-Fu Liu

Viruses 2023, 15(7), 1562; https://doi.org/10.3390/v15071562 - 16 Jul 2023

Cited by 2 | Viewed by 1798

Abstract

We developed a convenient method for amplifying the complete SARS-CoV-2 sequence using in-house RT-PCR without virus culture. Forty-one stored throat swabs and blood specimens were collected from eight SARS-CoV-2 infections at multiple time points. Total RNA was extracted using the QIAamp viral RNA [...] Read more.

We developed a convenient method for amplifying the complete SARS-CoV-2 sequence using in-house RT-PCR without virus culture. Forty-one stored throat swabs and blood specimens were collected from eight SARS-CoV-2 infections at multiple time points. Total RNA was extracted using the QIAamp viral RNA mini kit and pooled for higher RNA levels. Only those positive specimens by commercial real-time RT-PCR (RT-qPCR) were selected and amplified by in-house RT-PCR for complete sequences, followed by sequencing. Phylogenetic trees and exploratory analyses were performed using MEGA 11 and Simplot 3.5.1 software. Swab samples had significantly higher total RNA concentrations than plasma (p < 0.01). Positive results were found mainly in swabs, but one was found in plasma. Successful gene amplification depended on Ct values (Ct < 38). A non-synonymous substitution was found in ORF1ab/Nsp3 (at NC045512.2 position 6312, C to A) and most spike protein mutations occurred in the S1 subunit (residues 14–685). The proposed method is time-saving and reliable for rapid genomic analysis. Increasing sample volume and pooling them for RNA extraction increases RNA concentration without culture. Combining nucleotide sequences from specific variable regions of the genome is more efficient than conventional methods. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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18 pages, 5795 KiB

Open AccessArticle

SARS-CoV-2 Reinfections in Health-Care Workers, 1 March 2020–31 January 2023

by Luca Cegolon, Greta Magnano, Corrado Negro and Francesca Larese Filon

Viruses 2023, 15(7), 1551; https://doi.org/10.3390/v15071551 - 14 Jul 2023

Cited by 27 | Viewed by 3538

Abstract

Objective: To study SARS-CoV-2 reinfections in health-care workers (HCWs) of the University Health Agency Giuliano-Isontina (ASUGI), covering the provinces of Trieste and Gorizia (northeastern Italy) routinely screened for SARS-CoV-2 via nasopharyngeal swab. Design: Cohort study of HCWs (N = 8205) followed since the [...] Read more.

Objective: To study SARS-CoV-2 reinfections in health-care workers (HCWs) of the University Health Agency Giuliano-Isontina (ASUGI), covering the provinces of Trieste and Gorizia (northeastern Italy) routinely screened for SARS-CoV-2 via nasopharyngeal swab. Design: Cohort study of HCWs (N = 8205) followed since the start of the pandemic (1 March 2020) through 31 January 2023. The risk of reinfection during the Omicron transmission period (after 30 November 2021) among HCWs previously infected by SARS-CoV-2 was estimated based on days since last dose of COVID-19 vaccine received, adjusting for age, sex, job task, workplace, number of doses of COVID-19 vaccines and number of swab tests performed. In the crude as well as adjusted incidence rate analysis, reinfections occurring 15+ days after a first dose of COVID-19 vaccine or 8+ days following a second or more dose were counted. Results: In a highly vaccinated population, during the entire study period (1 March 2020–31 January 2023) 5253 HCWs incurred at least one SARS-CoV-2 infection, 4262 HCWs were infected only once, and 1091 were reinfected. Reinfections almost entirely (99.1% = 1071/1091) occurred after 30 November 2021, peaking in July 2022 (N = 161). Six hundred eighty-three reinfections followed a pre-Omicron primary event against 408 reinfections following an Omicron event. Reinfections during the Omicron transmission period occurred a mean of 400 ± 220 days after primary SARS-CoV-2 infection; 512 ± 205 days following a pre-Omicron primary event, as opposed to 218 ± 74 days after an Omicron primary infection. Thirty-four hospitalizations were observed, all before the Omicron wave, following 18 (0.4%) primary SARS-CoV-2 infections and 16 (1.5%) reinfections. By excluding events occurring <15 days after a first dose or <8 days after a further dose of COVID-19 vaccine, 605 reinfections followed a pre-Omicron primary event (raw incidence = 1.4 × 1000 person-days) against 404 after a primary Omicron infection (raw incidence = 0.3 × 1000 person-days). Apart from nurse aids (slightly enhanced biological risk) and academic HCWs (remarkably lower risk with pre-Omicron primary events), the effect of occupation in terms of job task and workplace was marginal. Furthermore, whilst the risk of reinfection was lower in males and HCWs < 60 years old following a pre-Omicron primary infection, HCWs aged 30–50 were more likely to be infected after an Omicron primary event. Regardless of timeline of primary SARS-CoV-2 event, the risk of reinfection decreased with higher number of doses of COVID-19 vaccines, being lowest after the second booster. In particular, VE was 16% for one dose, 51% for two doses, 76% for the booster and 92% for the second booster with a pre-Omicron primary SARS-CoV-2 event. The latter figures increased to 72%, 59%, 74% and 93%, respectively, with Omicron primary infections. Conclusions: SARS-CoV-2 reinfections were frequent during the Omicron transmission period, though featured by mild or no symptoms. Whilst the impact of occupation on biological risk was relatively marginal, COVID-19 vaccination had the strongest protective effect against reinfection, with a 93% VE by second booster following an Omicron primary infection. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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12 pages, 4063 KiB

Open AccessArticle

Dissemination of the Omicron Variant and Its Sub-Lineages among Residents and Travelers in Its First Year of Emergence in Venezuela

by Zoila C. Moros, José Luis Zambrano, Yoneira Sulbaran, Carmen L. Loureiro, Ernestina Marulanda, Francis Bracho, Pierina D’Angelo, Lieska Rodríguez, Ferdinando Liprandi, Héctor R. Rangel, Rossana C. Jaspe and Flor H. Pujol

Viruses 2023, 15(7), 1460; https://doi.org/10.3390/v15071460 - 28 Jun 2023

Viewed by 1277

Abstract

The emergence of the SARS-CoV-2 Variant of Concern (VOC), Omicron, has been characterized by an explosive number of cases in almost every part of the world. The dissemination of different sub-lineages and recombinant genomes also led to several posterior waves in many countries. [...] Read more.

The emergence of the SARS-CoV-2 Variant of Concern (VOC), Omicron, has been characterized by an explosive number of cases in almost every part of the world. The dissemination of different sub-lineages and recombinant genomes also led to several posterior waves in many countries. The circulation of this VOC and its major sub-lineages (BA.1 to BA.5) was monitored in community cases and in international travelers returning to Venezuela by a rapid partial sequencing method. The specific sub-lineage assignment was performed by complete genome sequencing. Epidemic waves of SARS-CoV-2 cases were observed among international travelers during 2022, a situation not seen before December 2021. The succession of the Omicron VOC sub-lineages BA.1 to BA.5 occurred sequentially, except for BA.3, which was almost not detected. However, the sub-lineages generally circulated two months earlier in international travelers than in community cases. The diversity of Omicron sub-lineages found in international travelers was related to the one found in the USA, consistent with the most frequent destination of international travel from Venezuela this year. These differences are compatible with the delay observed sometimes in Latin American countries in the circulation of the different lineages of the Omicron VOC. Once the sub-lineages were introduced in the country, community transmission was responsible for generating a characteristic distribution of them, with a predominance of sub-lineages not necessarily similar to the one observed in travelers or neighboring countries. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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10 pages, 2027 KiB

Open AccessCommunication

An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint Petersburg, Russia

by Galya V. Klink, Daria Danilenko, Andrey B. Komissarov, Nikita Yolshin, Olga Shneider, Sergey Shcherbak, Elena Nabieva, Nikita Shvyrev, Nadezhda Konovalova, Alyona Zheltukhina, Artem Fadeev, Kseniya Komissarova, Andrey Ksenafontov, Tamila Musaeva, Veronika Eder, Maria Pisareva, Petr Nekrasov, Vladimir Shchur, Georgii A. Bazykin and Dmitry Lioznov

Viruses 2023, 15(7), 1415; https://doi.org/10.3390/v15071415 - 22 Jun 2023

Cited by 2 | Viewed by 2208

Abstract

The Omicron variant of SARS-CoV-2 rapidly spread worldwide in late 2021–early 2022, displacing the previously prevalent Delta variant. Before 16 December 2021, community transmission had already been observed in tens of countries globally. However, in Russia, the majority of reported cases at that [...] Read more.

The Omicron variant of SARS-CoV-2 rapidly spread worldwide in late 2021–early 2022, displacing the previously prevalent Delta variant. Before 16 December 2021, community transmission had already been observed in tens of countries globally. However, in Russia, the majority of reported cases at that time had been sporadic and associated with travel. Here, we report an Omicron outbreak at a student dormitory in Saint Petersburg between 16–29 December 2021, which was the earliest known instance of a large-scale community transmission in Russia. Out of the 465 sampled residents of the dormitory, 180 (38.7%) tested PCR-positive. Among the 118 residents for whom the variant had been tested by whole-genome sequencing, 111 (94.1%) were found to carry the Omicron variant. Among these 111 residents, 60 (54.1%) were vaccinated or had reported a previous infection of COVID-19. Phylogenetic analysis confirmed that the outbreak was caused by a single introduction of the BA.1.1 sub-lineage of the Omicron variant. The dormitory-derived clade constituted a significant proportion of BA.1.1 samples in Saint Petersburg and has spread to other regions of Russia and even to other countries. The rapid spread of the Omicron variant in a population with preexisting immunity to previous variants underlines its propensity for immune evasion. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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18 pages, 2151 KiB

Open AccessArticle

The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37

by Mercedes Soledad Nabaes Jodar, Carolina Torres, Laura Mojsiejczuk, Dolores Acuña, Laura Elena Valinotto, Stephanie Goya, Monica Natale, Silvina Lusso, Sofia Alexay, Ariel Amadio, Matias Irazoqui, Franco Fernandez, Maria Elina Acevedo, Cristina Alvarez Lopez, Andres Angelletti, Paula Aulicino, Elisa Bolatti, Bettina Brusés, Marco Cacciahue, Ana Cavatorta, Agustina Cerri, Andres Cordero, Humberto Debat, Maria Jose Dus Santos, Maria Florencia Eberhardt, Regina Ercole, Carlos Espul, Marisa Farber, Fabián Fay, Ailen Fernandez, Florencia Ferrini, Laura Formichelli, Santiago Ceballos, Fernando Gallego, Adriana Giri, Maria Gismondi, Raul Maximiliano Acevedo, Ivan Gramundi, María Eugenia Ibañez, Guido Konig, Viviana Leiva, Melina Lorenzini Campos, Horacio Lucero, Nathalie Marquez, Melina Mazzeo, Alicia Susana Mistchenko, Luciana Montoto, Marianne Muñoz, Victoria Nadalich, Cristina Nardi, Belén Ortiz, Luis Pianciola, Carolina Pintos, Andrea Puebla, Carolina Rastellini, Alejandro Ezequiel Rojas, Javier Sfalcin, Ariel Suarez, Clara Theaux, Guillermo Thomas, Estefania Tittarelli, Rosana Toro, Vanina Villanova, Gretel Wenk, Cecilia Ziehm, Maria Carla Zimmermann, Sebastian Zunino, Proyecto PAIS and Mariana Viegas Show full author list Hide full author list

Viruses 2023, 15(6), 1382; https://doi.org/10.3390/v15061382 - 16 Jun 2023

Cited by 2 | Viewed by 2645

Abstract

The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its [...] Read more.

The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its initial entry into the country until its detection ceased. Molecular surveillance was conducted on 9356 samples from Argentina between October 2020 and April 2022, and sequencing, phylogenetic, and phylogeographic analyses were performed. Our findings revealed that the Lambda variant was first detected in Argentina in January 2021 and steadily increased in frequency until it peaked in April 2021, with continued detection throughout the year. Phylodynamic analyses showed that at least 18 introductions of the Lambda variant into the country occurred, with nine of them having evidence of onward local transmission. The spatial–-temporal reconstruction showed that Argentine clades were associated with Lambda sequences from Latin America and suggested an initial diversification in the Metropolitan Area of Buenos Aires before spreading to other regions in Argentina. Genetic analyses of genome sequences allowed us to describe the mutational patterns of the Argentine Lambda sequences and detect the emergence of rare mutations in an immunocompromised patient. Our study highlights the importance of genomic surveillance in identifying the introduction and geographical distribution of the SARS-CoV-2 Lambda variant, as well as in monitoring the emergence of mutations that could be involved in the evolutionary leaps that characterize variants of concern. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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10 pages, 1467 KiB

Open AccessArticle

Genomic Surveillance of SARS-CoV-2 Variants That Emerged in South and Southeast Asia during Early 2022

by Qiong Yu, Xi Tong, Li Zuo, Xinyu Tao, Zhonghui Xu, Xiaocui Li, Haizhou Liu, Wuxiang Guan, Di Liu, Haibin Liu, Fang Huang and Lijia Jia

Viruses 2023, 15(6), 1355; https://doi.org/10.3390/v15061355 - 12 Jun 2023

Cited by 1 | Viewed by 2004

Abstract

The continuously emerging new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have made the global coronavirus disease 2019 (COVID-19) pandemic unpredictable. Since the beginning of the pandemic, densely populated South and Southeast Asia have suffered great losses due to multiple COVID-19 [...] Read more.

The continuously emerging new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have made the global coronavirus disease 2019 (COVID-19) pandemic unpredictable. Since the beginning of the pandemic, densely populated South and Southeast Asia have suffered great losses due to multiple COVID-19 surges because of vaccine and other medical resource shortages. Therefore, it is crucial to closely monitor the SARS-CoV-2 epidemic and to understand the evolutionary and transmission characteristics of SARS-CoV-2 in these regions. Here, we document the evolution of epidemic strains in the Philippines, Pakistan, and Malaysia from late 2021 to early 2022. Our results confirmed the circulation of at least five SARS-CoV-2 genotypes in these countries in January 2022, when Omicron BA.2, with a detection rate of 69.11%, replaced Delta B.1.617 as the dominant strain. Single-nucleotide polymorphism analysis indicated the distinct evolutionary directions of the Omicron and Delta isolates, with S, Nsp1, and Nsp6 genes potentially playing a significant role in the host adaptation of the Omicron strain. These findings are able to provide insights for predicting the evolutionary direction of SARS-CoV-2 in terms of variant competition, developing multi-part vaccines, and to support the evaluation and adjustment of current surveillance, prevention, and control strategies in South and Southeast Asia. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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13 pages, 2450 KiB

Open AccessArticle

Genomic Epidemiology of SARS-CoV-2 in Urban Settings in Senegal

by Anna Julienne Selbé Ndiaye, Mamadou Beye, Gora Lo, Idir Kacel, Aissatou Sow, Nafissatou Leye, Abdou Padane, Aminata Mboup, Halimatou Diop-Ndiaye, Cheikh Sokhna, Coumba Touré Kane, Philippe Colson, Florence Fenollar, Souleymane Mboup and Pierre-Edouard Fournier

Viruses 2023, 15(6), 1233; https://doi.org/10.3390/v15061233 - 24 May 2023

Cited by 1 | Viewed by 2289

Abstract

We used whole genome sequencing to identify and analyze mutations in SARS-CoV-2 in urban settings during the deadliest wave of the COVID-19 epidemic—from March to April 2021—in Senegal. Nasopharyngeal samples testing positive for SARS-CoV-2 were sequenced on the Illumina NovaSeq 6000 sequencing system [...] Read more.

We used whole genome sequencing to identify and analyze mutations in SARS-CoV-2 in urban settings during the deadliest wave of the COVID-19 epidemic—from March to April 2021—in Senegal. Nasopharyngeal samples testing positive for SARS-CoV-2 were sequenced on the Illumina NovaSeq 6000 sequencing system using the COVIDSeq protocol. A total of 291 genotypable consensus genome sequences were obtained. Phylogenetic analyses grouped the genomes into 16 distinct PANGOLIN lineages. The major lineage was B.1.1.420, despite circulation of the Alpha variant of concern (VOC). A total of 1125 different SNPs, identified relative to the Wuhan reference genome, were detected. These included 13 SNPs in non-coding regions. An average density of 37.2 SNPs per 1000 nucleotides was found, with the highest density occurring in ORF10. This analysis allowed, for the first time, the detection of a Senegalese SARS-CoV-2 strain belonging to the P.1.14 (GR/20J, Gamma V3) sublineage of the Brazilian P.1 lineage (or Gamma VOC). Overall, our results highlight substantial SARS-CoV-2 diversification in Senegal during the study period. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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13 pages, 2131 KiB

Open AccessArticle

Immune Factors Drive Expression of SARS-CoV-2 Receptor Genes Amid Sexual Disparity

by Ashutosh Vashisht, Pankaj Ahluwalia, Ashis K. Mondal, Harmanpreet Singh, Nikhil S. Sahajpal, Sadanand Fulzele, Vamsi Kota, Gagandeep K. Gahlay and Ravindra Kolhe

Viruses 2023, 15(3), 657; https://doi.org/10.3390/v15030657 - 28 Feb 2023

Cited by 1 | Viewed by 2252

Abstract

The emergence of COVID-19 has led to significant morbidity and mortality, with around seven million deaths worldwide as of February 2023. There are several risk factors such as age and sex that are associated with the development of severe symptoms due to COVID-19. [...] Read more.

The emergence of COVID-19 has led to significant morbidity and mortality, with around seven million deaths worldwide as of February 2023. There are several risk factors such as age and sex that are associated with the development of severe symptoms due to COVID-19. There have been limited studies that have explored the role of sex differences in SARS-CoV-2 infection. As a result, there is an urgent need to identify molecular features associated with sex and COVID-19 pathogenesis to develop more effective interventions to combat the ongoing pandemic. To address this gap, we explored sex-specific molecular factors in both mouse and human datasets. The host immune targets such as TLR7, IRF7, IRF5, and IL6, which are involved in the immune response against viral infections, and the sex-specific targets such as AR and ESSR were taken to investigate any possible link with the SARS-CoV-2 host receptors ACE2 and TMPRSS2. For the mouse analysis, a single-cell RNA sequencing dataset was used, while bulk RNA-Seq datasets were used to analyze the human clinical data. Additional databases such as the Database of Transcription Start Sites (DBTS), STRING-DB, and the Swiss Regulon Portal were used for further analysis. We identified a 6-gene signature that showed differential expression in males and females. Additionally, this gene signature showed potential prognostic utility by differentiating ICU patients from non-ICU patients due to COVID-19. Our study highlights the importance of assessing sex differences in SARS-CoV-2 infection, which can assist in the optimal treatment and better vaccination strategies. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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17 pages, 4841 KiB

Open AccessArticle

Evaluating Data Sharing of SARS-CoV-2 Genomes for Molecular Epidemiology across the COVID-19 Pandemic

by Teresa Rito, Pedro Fernandes, Raquel Duarte and Pedro Soares

Viruses 2023, 15(2), 560; https://doi.org/10.3390/v15020560 - 17 Feb 2023

Cited by 3 | Viewed by 2302

Abstract

Following the emergence of COVID-19 in December 2019, caused by the coronavirus SARS-CoV-2, the disease spread dramatically worldwide. The use of genomics to trace the dissemination of the virus and the identification of novel variants was essential in defining measures for containing the [...] Read more.

Following the emergence of COVID-19 in December 2019, caused by the coronavirus SARS-CoV-2, the disease spread dramatically worldwide. The use of genomics to trace the dissemination of the virus and the identification of novel variants was essential in defining measures for containing the disease. We aim to evaluate the global effort to genomically characterize the circulating lineages of SARS-CoV-2, considering the data deposited in GISAID, the major platform for data sharing in a massive worldwide collaborative undertaking. We contextualize data for nearly three years (January 2020–October 2022) for the major contributing countries, percentage of characterized isolates and time for data processing in the context of the global pandemic. Within this collaborative effort, we also evaluated the early detection of seven major SARS-CoV-2 lineages, G, GR, GH, GK, GV, GRY and GRA. While Europe and the USA, following an initial period, showed positive results across time in terms of cases sequenced and time for data deposition, this effort is heterogeneous worldwide. Given the current immunization the major threat is the appearance of variants that evade the acquired immunity. In that scenario, the monitoring of those hypothetical variants will still play an essential role. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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12 pages, 3348 KiB

Open AccessArticle

Persistence of a Frameshifting Deletion in SARS-CoV-2 ORF7a for the Duration of a Major Outbreak

by Charles S. P. Foster, Rowena A. Bull, Nicodemus Tedla, Fernando Santiago, David Agapiou, Anurag Adhikari, Gregory J. Walker, Lok Bahadur Shrestha, Sebastiaan J. Van Hal, Ki Wook Kim and William D. Rawlinson

Viruses 2023, 15(2), 522; https://doi.org/10.3390/v15020522 - 13 Feb 2023

Cited by 3 | Viewed by 2973

Abstract

Australia experienced widespread COVID-19 outbreaks from infection with the SARS-CoV-2 Delta variant between June 2021 and February 2022. A 17-nucleotide frameshift-inducing deletion in ORF7a rapidly became represented at the consensus level (Delta-ORF7a^Δ17del) in most Australian outbreak cases. Studies from early in [...] Read more.

Australia experienced widespread COVID-19 outbreaks from infection with the SARS-CoV-2 Delta variant between June 2021 and February 2022. A 17-nucleotide frameshift-inducing deletion in ORF7a rapidly became represented at the consensus level (Delta-ORF7a^Δ17del) in most Australian outbreak cases. Studies from early in the COVID-19 pandemic suggest that frameshift-inducing deletions in ORF7a do not persist for long in the population; therefore, Delta-ORF7a^Δ17del genomes should have disappeared early in the Australian outbreak. In this study, we conducted a retrospective analysis of global Delta genomes to characterise the dynamics of Delta-ORF7a^Δ17del over time, determined the frequency of all ORF7a deletions worldwide, and compared global trends with those of the Australian Delta outbreak. We downloaded all GISAID clade GK Delta genomes and scanned them for deletions in ORF7a. For each deletion we identified, we characterised its frequency, the number of countries it was found in, and how long it persisted. Of the 4,018,216 Delta genomes identified globally, 134,751 (~3.35%) possessed an ORF7a deletion, and ORF7a^Δ17del was the most common. ORF7a^Δ17del was the sole deletion in 28,014 genomes, of which 27,912 (~99.6%) originated from the Australian outbreak. During the outbreak, ~87% of genomes were Delta-ORF7a^Δ17del, and genomes with this deletion were sampled until the outbreak’s end. These data demonstrate that, contrary to suggestions early in the COVID-19 pandemic, genomes with frameshifting deletions in ORF7a can persist over long time periods. We suggest that the proliferation of Delta-ORF7a^Δ17del genomes was likely a chance founder effect. Nonetheless, the frequency of ORF7a deletions in SARS-CoV-2 genomes worldwide suggests they might have some benefit for virus transmission. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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10 pages, 3731 KiB

Open AccessCommunication

Rapid System to Detect Variants of SARS-CoV-2 in Nasopharyngeal Swabs

by Marco Favaro, Paola Zampini, Enrico Salvatore Pistoia, Roberta Gaziano, Sandro Grelli and Carla Fontana

Viruses 2023, 15(2), 353; https://doi.org/10.3390/v15020353 - 26 Jan 2023

Viewed by 1815

Abstract

Currently, the reference method for identifying the presence of variants of SARS-CoV-2 is whole genome sequencing. Although it is less expensive than in the past, it is still time-consuming, and interpreting the results is difficult, requiring staff with specific skills who are not [...] Read more.

Currently, the reference method for identifying the presence of variants of SARS-CoV-2 is whole genome sequencing. Although it is less expensive than in the past, it is still time-consuming, and interpreting the results is difficult, requiring staff with specific skills who are not always available in diagnostic laboratories. The test presented in this study aimed to detect, using traditional real-time PCR, the presence of the main variants described for the spike protein of the SARS-CoV-2 genome. The primers and probes were designed to detect the main deletions that characterize the different variants. The amplification targets were deletions in the S gene: 25–27, 69–70, 241–243, and 157–158. In the ORF1a gene, the deletion 3675–3677 was chosen. Some of these mutations can be considered specific variants, while others can be identified by the simultaneous presence of one or more deletions. We avoided using point mutations in order to improve the speed of the test. Our test can help clinical and medical microbiologists quickly recognize the presence of variants in biological samples (particularly nasopharyngeal swabs). The test can also be used to identify variants of the virus that could potentially be more diffusive as well as not responsive to the vaccine. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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10 pages, 1484 KiB

Open AccessCommunication

Retrospective Insights of the COVID-19 Epidemic in the Major Latin American City, São Paulo, Southeastern Brazil

by Patricia Akemi Assato, Luan Gaspar Clemente, Marta Giovanetti, Gabriela Ribeiro, Alex Ranieri Jeronimo Lima, Melissa Palmieri, Leonardo Nazario de Moraes, Simone Kashima, Heidge Fukumasu, Maurício Lacerda Nogueira, Luiz Carlos Junior Alcantara, Aline Lais Nicolodelli, Antonio Jorge Martins, Bruna Petry, Cecilia Artico Banho, Claudia Renata Dos Santos Barros, Cristina Tschorny Moncau-Gadbem, Debora Botequio Moretti, Debora Glenda Lima De La Roque, Elaine Cristina Marqueze, Elisangela Chicaroni Mattos, Fabiana Erica Vilanova Da Silva, Felipe Allan Da Silva Da Costa, Giselle Cacherik, Jardelina De Souza Todao Bernardino, Jessika Cristina Chagas Lesbon, Lívia Sacchetto, Loyze Paola Oliveira De Lima, Luiz Artur Vieira Caldeira, Maiara Martininghi, Marília Mazzi Moraes, Mirele Daiana Poleti, Pedro De Queiroz Cattony Neto, Raquel De Lello Rocha Campos Cassano, Ricardo Augusto Brassaloti, Svetoslav Nanev Slavov, Vincent Louis Viala, Luiz Lehmann Coutinho, Rejane Maria Tommasini Grotto, Raul Machado Neto, Dimas Tadeu Covas, Sandra Coccuzzo Sampaio, Maria Carolina Elias and Jayme A. Souza-Neto Show full author list Hide full author list

Viruses 2023, 15(2), 327; https://doi.org/10.3390/v15020327 - 24 Jan 2023

Cited by 2 | Viewed by 2651

Abstract

São Paulo is the financial center of Brazil, with a population of over 12 million, that receives travelers from all over the world for business and tourism. It was the first city in Brazil to report a case of COVID-19 that rapidly spread [...] Read more.

São Paulo is the financial center of Brazil, with a population of over 12 million, that receives travelers from all over the world for business and tourism. It was the first city in Brazil to report a case of COVID-19 that rapidly spread across the city despite the implementation of the restriction measures. Despite many reports, much is still unknown regarding the genomic diversity and transmission dynamics of this virus in the city of São Paulo. Thus, in this study, we provide a retrospective overview of the COVID-19 epidemic in São Paulo City, Southeastern, Brazil, by generating a total of 9995 near-complete genome sequences from all the city’s different macro-regions (North, West, Central, East, South, and Southeast). Our analysis revealed that multiple independent introduction events of different variants (mainly Gamma, Delta, and Omicron) occurred throughout time. Additionally, our estimates of viral movement within the different macro-regions further suggested that the East and the Southeast regions were the largest contributors to the Gamma and Delta viral exchanges to other regions. Meanwhile, the North region had a higher contribution to the dispersion of the Omicron variant. Together, our results reinforce the importance of increasing SARS-CoV-2 genomic monitoring within the city and the country to track the real-time evolution of the virus and to detect earlier any eventual emergency of new variants of concern that could undermine the fight against COVID-19 in Brazil and worldwide. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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22 pages, 39559 KiB

Open AccessArticle

Molecular Epidemiology of SARS-CoV-2: The Dominant Role of Arginine in Mutations and Infectivity

by Harry Ridgway, Charalampos Ntallis, Christos T. Chasapis, Konstantinos Kelaidonis, Minos-Timotheos Matsoukas, Panagiotis Plotas, Vasso Apostolopoulos, Graham Moore, Sotirios Tsiodras, Dimitrios Paraskevis, Thomas Mavromoustakos and John M. Matsoukas

Viruses 2023, 15(2), 309; https://doi.org/10.3390/v15020309 - 22 Jan 2023

Cited by 15 | Viewed by 3518

Abstract

Background, Aims, Methods, Results, Conclusions: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global challenge due to its ability to mutate into variants that spread more rapidly than the wild-type virus. The molecular biology of this virus has [...] Read more.

Background, Aims, Methods, Results, Conclusions: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global challenge due to its ability to mutate into variants that spread more rapidly than the wild-type virus. The molecular biology of this virus has been extensively studied and computational methods applied are an example paradigm for novel antiviral drug therapies. The rapid evolution of SARS-CoV-2 in the human population is driven, in part, by mutations in the receptor-binding domain (RBD) of the spike (S-) protein, some of which enable tighter binding to angiotensin-converting enzyme (ACE2). More stable RBD-ACE2 association is coupled with accelerated hydrolysis by proteases, such as furin, trypsin, and the Transmembrane Serine Protease 2 (TMPRSS2) that augment infection rates, while inhibition of the 3-chymotrypsin-like protease (3CL^pro) can prevent the viral replication. Additionally, non-RBD and non-interfacial mutations may assist the S-protein in adopting thermodynamically favorable conformations for stronger binding. This study aimed to report variant distribution of SARS-CoV-2 across European Union (EU)/European Economic Area (EEA) countries and relate mutations with the driving forces that trigger infections. Variants’ distribution data for SARS-CoV-2 across EU/EEA countries were mined from the European Centre for Disease Prevention and Control (ECDC) based on the sequence or genotyping data that are deposited in the Global Science Initiative for providing genomic data (GISAID) and The European Surveillance System (TESSy) databases. Docking studies performed with AutoDock VINA revealed stabilizing interactions of putative antiviral drugs, e.g., selected anionic imidazole biphenyl tetrazoles, with the ACE2 receptor in the RBD-ACE2 complex. The driving forces of key mutations for Alpha, Beta, Gamma, Delta, Epsilon, Kappa, Lambda, and Omicron variants, which stabilize the RBD-ACE2 complex, were investigated by computational approaches. Arginine is the critical amino acid in the polybasic furin cleavage sites S1/S2 (681-PRRARS-686) S2′ (814-KRS-816). Critical mutations into arginine residues that were found in the delta variant (L452R, P681R) and may be responsible for the increased transmissibility and morbidity are also present in two widely spreading omicron variants, named BA.4.6 and BQ.1, where mutation R346T in the S-protein potentially contributes to neutralization escape. Arginine binders, such as Angiotensin Receptor Blockers (ARBs), could be a class of novel drugs for treating COVID-19. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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16 pages, 2368 KiB

Open AccessArticle

Origin, Genetic Variation and Molecular Epidemiology of SARS-CoV-2 Strains Circulating in Sardinia (Italy) during the First and Second COVID-19 Epidemic Waves

by Angela Maria Rocchigiani, Luca Ferretti, Alice Ledda, Antonello Di Nardo, Matteo Floris, Piero Bonelli, Federica Loi, Maria Laura Idda, Pier Paolo Angioi, Susanna Zinellu, Mariangela Stefania Fiori, Roberto Bechere, Paola Capitta, Annamaria Coccollone, Elisabetta Coradduzza, Maria Antonietta Dettori, Maria Caterina Fattaccio, Elena Gallisai, Caterina Maestrale, Daniela Manunta, Aureliana Pedditzi, Ivana Piredda, Bruna Palmas, Sara Salza, Anna Maria Sechi, Barbara Tanda, Maria Paola Madrau, Maria Luisa Sanna, Simonetta Cherchi, Nicoletta Ponti, Giovanna Masala, Roberto Sirica, Eloisa Evangelista, Annalisa Oggiano, Giantonella Puggioni, Ciriaco Ligios and Silvia Dei Giudici Show full author list Hide full author list

Viruses 2023, 15(2), 277; https://doi.org/10.3390/v15020277 - 18 Jan 2023

Cited by 2 | Viewed by 2893

Abstract

Understanding how geography and human mobility shape the patterns and spread of infectious diseases such as COVID-19 is key to control future epidemics. An interesting example is provided by the second wave of the COVID-19 epidemic in Europe, which was facilitated by the [...] Read more.

Understanding how geography and human mobility shape the patterns and spread of infectious diseases such as COVID-19 is key to control future epidemics. An interesting example is provided by the second wave of the COVID-19 epidemic in Europe, which was facilitated by the intense movement of tourists around the Mediterranean coast in summer 2020. The Italian island of Sardinia is a major tourist destination and is widely believed to be the origin of the second Italian wave. In this study, we characterize the genetic variation among SARS-CoV-2 strains circulating in northern Sardinia during the first and second Italian waves using both Illumina and Oxford Nanopore Technologies Next Generation Sequencing methods. Most viruses were placed into a single clade, implying that despite substantial virus inflow, most outbreaks did not spread widely. The second epidemic wave on the island was actually driven by local transmission of a single B.1.177 subclade. Phylogeographic analyses further suggest that those viral strains circulating on the island were not a relevant source for the second epidemic wave in Italy. This result, however, does not rule out the possibility of intense mixing and transmission of the virus among tourists as a major contributor to the second Italian wave. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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14 pages, 2728 KiB

Open AccessArticle

Omicron-BA.1 Dispersion Rates in Mexico Varied According to the Regional Epidemic Patterns and the Diversity of Local Delta Subvariants

by Selene Zárate, Blanca Taboada, Mauricio Rosales-Rivera, Rodrigo García-López, José Esteban Muñoz-Medina, Alejandro Sanchez-Flores, Alfredo Herrera-Estrella, Bruno Gómez-Gil, Nelly Selem Mojica, Angel Gustavo Salas-Lais, Joel Armando Vazquez-Perez, David Alejandro Cabrera-Gaytán, Larissa Fernandes-Matano, Luis Antonio Uribe-Noguez, Juan Bautista Chale-Dzul, Brenda Irasema Maldonado Meza, Fidencio Mejía-Nepomuceno, Rogelio Pérez-Padilla, Rosa María Gutiérrez-Ríos, Antonio Loza, Benjamin Roche, Susana López and Carlos F. Arias Show full author list Hide full author list

Viruses 2023, 15(1), 243; https://doi.org/10.3390/v15010243 - 15 Jan 2023

Cited by 6 | Viewed by 3110

Abstract

Purpose: The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In this work, a characterization of the spread of this variant in Mexico is presented. Methods: The time to fixation of BA.1, [...] Read more.

Purpose: The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In this work, a characterization of the spread of this variant in Mexico is presented. Methods: The time to fixation of BA.1, the diversity of Delta sublineages, the population density, and the level of virus circulation during the inter-wave interval were determined to analyze differences in BA.1 spread. Results: BA.1 began spreading during the first week of December 2021 and became dominant in the next three weeks, causing the fourth COVID-19 epidemiological surge in Mexico. Unlike previous variants, BA.1 did not exhibit a geographically distinct circulation pattern. However, a regional difference in the speed of the replacement of the Delta variant was observed. Conclusions: Viral diversity and the relative abundance of the virus in a particular area around the time of the introduction of a new lineage seem to have influenced the spread dynamics, in addition to population density. Nonetheless, if there is a significant difference in the fitness of the variants, or if the time allowed for the competition is sufficiently long, it seems the fitter virus will eventually become dominant, as observed in the eventual dominance of the BA.1.x variant in Mexico. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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12 pages, 2797 KiB

Open AccessCommunication

A Repeat Pattern of Founder Events for SARS-CoV-2 Variants in Alaska

by Tracie J. Haan, Lisa K. Smith, Stephanie DeRonde, Elva House, Jacob Zidek, Diana Puhak, Logan Mullen, Matthew Redlinger, Jayme Parker, Brian M. Barnes, Jason L. Burkhead, Cindy Knall, Eric Bortz, Jack Chen and Devin M. Drown

Viruses 2023, 15(1), 222; https://doi.org/10.3390/v15010222 - 13 Jan 2023

Cited by 2 | Viewed by 2410

Abstract

Alaska is a unique US state because of its large size, geographically disparate population density, and physical distance from the contiguous United States. Here, we describe a pattern of SARS-CoV-2 variant emergence across Alaska reflective of these differences. Using genomic data, we found [...] Read more.

Alaska is a unique US state because of its large size, geographically disparate population density, and physical distance from the contiguous United States. Here, we describe a pattern of SARS-CoV-2 variant emergence across Alaska reflective of these differences. Using genomic data, we found that in Alaska, the Omicron sublineage BA.2.3 overtook BA.1.1 by the week of 27 February 2022, reaching 48.5% of sequenced cases. On the contrary, in the contiguous United States, BA.1.1 dominated cases for longer, eventually being displaced by BA.2 sublineages other than BA.2.3. BA.2.3 only reached a prevalence of 10.9% in the contiguous United States. Using phylogenetics, we found evidence of potential origins of the two major clades of BA.2.3 in Alaska and with logistic regression estimated how it emerged and spread throughout the state. The combined evidence is suggestive of founder events in Alaska and is reflective of how Alaska’s unique dynamics influence the emergence of SARS-CoV-2 variants. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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30 pages, 5426 KiB

Open AccessArticle

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

by Andreas C. Chrysostomou, Bram Vrancken, Christos Haralambous, Maria Alexandrou, Antonia Aristokleous, Christina Christodoulou, Ioanna Gregoriou, Marios Ioannides, Olga Kalakouta, Christos Karagiannis, George Koumbaris, Charalambos Loizides, Michail Mendris, Panagiotis Papastergiou, Philippos C. Patsalis, Despo Pieridou, Jan Richter, Markus Schmitt, Christos Shammas, Dora C. Stylianou, Giorgos Themistokleous, the COMESSAR Network, Philippe Lemey and Leondios G. Kostrikis Show full author list Hide full author list

Viruses 2023, 15(1), 108; https://doi.org/10.3390/v15010108 - 30 Dec 2022

Cited by 5 | Viewed by 5567

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in [...] Read more.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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12 pages, 899 KiB

Open AccessArticle

Genomic Epidemiology of SARS-CoV-2 in Western Burkina Faso, West Africa

by Yacouba Sawadogo, Lokman Galal, Essia Belarbi, Arsène Zongo, Grit Schubert, Fabian Leendertz, Abdoulie Kanteh, Abdul Karim Sesay, Annette Erhart, Anne-Laure Bañuls, Zékiba Tarnagda, Sylvain Godreuil, Halidou Tinto and Abdoul-Salam Ouedraogo

Viruses 2022, 14(12), 2788; https://doi.org/10.3390/v14122788 - 14 Dec 2022

Cited by 4 | Viewed by 3051

Abstract

Background: After its initial detection in Wuhan, China, in December 2019, SARS-CoV-2 has spread rapidly, causing successive epidemic waves worldwide. This study aims to provide a genomic epidemiology of SARS-CoV-2 in Burkina Faso. Methods: Three hundred and seventy-seven SARS-CoV-2 genomes obtained from PCR-positive [...] Read more.

Background: After its initial detection in Wuhan, China, in December 2019, SARS-CoV-2 has spread rapidly, causing successive epidemic waves worldwide. This study aims to provide a genomic epidemiology of SARS-CoV-2 in Burkina Faso. Methods: Three hundred and seventy-seven SARS-CoV-2 genomes obtained from PCR-positive nasopharyngeal samples (PCR cycle threshold score < 35) collected between 5 May 2020, and 31 January 2022 were analyzed. Genomic sequences were assigned to phylogenetic clades using NextClade and to Pango lineages using pangolin. Phylogenetic and phylogeographic analyses were performed to determine the geographical sources and time of virus introduction in Burkina Faso. Results: The analyzed SARS-CoV-2 genomes can be assigned to 10 phylogenetic clades and 27 Pango lineages already described worldwide. Our analyses revealed the important role of cross-border human mobility in the successive SARS-CoV-2 introductions in Burkina Faso from neighboring countries. Conclusions: This study provides additional insights into the genomic epidemiology of SARS-CoV-2 in West Africa. It highlights the importance of land travel in the spread of the virus and the need to rapidly implement preventive policies. Regional cross-border collaborations and the adherence of the general population to government policies are key to prevent new epidemic waves. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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15 pages, 4086 KiB

Open AccessArticle

Monitoring the Establishment of VOC Gamma in Minas Gerais, Brazil: A Retrospective Epidemiological and Genomic Surveillance Study

by Hugo José Alves, João Locke Ferreira de Araújo, Paula Luize Camargos Fonseca, Filipe Romero Rebello Moreira, Diego Menezes Bonfim, Daniel Costa Queiroz, Lucyene Miguita, Rafael Marques de Souza, Victor Emmanuel Viana Geddes, Walyson Coelho Costa, Jaqueline Silva de Oliveira, Eva Lídia Arcoverde Medeiros, Carolina Senra Alves de Souza, Juliana Wilke Saliba, André Luiz Menezes, Eneida Santos de Oliveira, Talita Emile Ribeiro Adelino, Natalia Rocha Guimaraes, Adriana Aparecida Ribeiro, Rennan Garcias Moreira, Danielle Alves Gomes Zauli, Joice do Prado Silva, Frederico Scott Varella Malta, Alessandro Clayton de Souza Ferreira, Ana Valesca Fernandes Gilson Silva, Poliane Alfenas-Zerbini, Flavia Oliveira de Souza, Adriano de Paula Sabino, Laura do Amaral Xavier, Natália Virtude Carobin, Alex Fiorini de Carvalho, Karine Lima Lourenço, Santuza Maria Ribeiro Teixeira, Ana Paula Salles Moura Fernandes, Flavio Guimarães da Fonseca, Jônatas Santos Abrahão, Felipe Campos de Melo Iani, Rodrigo Araújo Lima Rodrigues, Renan Pedra de Souza and Renato Santana Aguiar Show full author list Hide full author list

Viruses 2022, 14(12), 2747; https://doi.org/10.3390/v14122747 - 9 Dec 2022

Cited by 3 | Viewed by 2737

Abstract

Since its first identification in Brazil, the variant of concern (VOC) Gamma has been associated with increased infection and transmission rates, hospitalizations, and deaths. Minas Gerais (MG), the second-largest populated Brazilian state with more than 20 million inhabitants, observed a peak of cases [...] Read more.

Since its first identification in Brazil, the variant of concern (VOC) Gamma has been associated with increased infection and transmission rates, hospitalizations, and deaths. Minas Gerais (MG), the second-largest populated Brazilian state with more than 20 million inhabitants, observed a peak of cases and deaths in March–April 2021. We conducted a surveillance study in 1240 COVID-19-positive samples from 305 municipalities distributed across MG’s 28 Regional Health Units (RHU) between 1 March to 27 April 2021. The most common variant was the VOC Gamma (71.2%), followed by the variant of interest (VOI) zeta (12.4%) and VOC alpha (9.6%). Although the predominance of Gamma was found in most of the RHUs, clusters of Zeta and Alpha variants were observed. One Alpha-clustered RHU has a history of high human mobility from countries with Alpha predominance. Other less frequent lineages, such as P.4, P.5, and P.7, were also identified. With our genomic characterization approach, we estimated the introduction of Gamma on 7 January 2021, at RHU Belo Horizonte. Differences in mortality between the Zeta, Gamma and Alpha variants were not observed. We reinforce the importance of vaccination programs to prevent severe cases and deaths during transmission peaks. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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13 pages, 1514 KiB

Open AccessArticle

Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April–December 2021 in Italy

by Alessia Lai, Annalisa Bergna, Carla Della Ventura, Stefano Menzo, Bianca Bruzzone, Fabio Sagradi, Francesca Ceccherini-Silberstein, Alessandro Weisz, Nicola Clementi, Gaetano Brindicci, Ilaria Vicenti, Lolita Sasset, Sara Caucci, Benedetta Corvaro, Silvia Ippoliti, Carla Acciarri, Vanessa De Pace, Leonardo Lanfranchi, Maria C. Bellocchi, Giorgio Giurato, Roberto Ferrarese, Antonella Lagioia, Daniela Francisci, Martina L. Colombo, Samuel Lazzarin, Matilde Ogliastro, Maria R. Cappelletti, Marco Iannetta, Francesca Rizzo, Carlo Torti, Maurizio Fumi, Morena d’Avenia, Stefano Brusa, Francesca Greco, Angela Menchise, Vittoria Letizia, Emilia Vaccaro, Carmen R. Santoro, Chiara Fraccalvieri, Sophie Testa, Luca Carioti, Teresa Rocco, Annalisa Saracino, Annamaria Cattelan, Massimo Clementi, Loredana Sarmati, Agostino Riva, Massimo Galli, Spinello Antinori, Gianguglielmo Zehender and SARS-CoV- ITALIAN RESEARCH ENTERPRISE–(SCIRE) Collaborative Group Show full author list Hide full author list

Viruses 2022, 14(11), 2508; https://doi.org/10.3390/v14112508 - 12 Nov 2022

Cited by 15 | Viewed by 3182

Abstract

SARS-CoV-2 is constantly evolving, leading to new variants. We analysed data from 4400 SARS-CoV-2-positive samples in order to pursue epidemiological variant surveillance and to evaluate their impact on public health in Italy in the period of April–December 2021. The main circulating strain (76.2%) [...] Read more.

SARS-CoV-2 is constantly evolving, leading to new variants. We analysed data from 4400 SARS-CoV-2-positive samples in order to pursue epidemiological variant surveillance and to evaluate their impact on public health in Italy in the period of April–December 2021. The main circulating strain (76.2%) was the Delta variant, followed by the Alpha (13.3%), the Omicron (5.3%), and the Gamma variants (2.9%). The B.1.1 lineages, Eta, Beta, Iota, Mu, and Kappa variants, represented around 1% of cases. There were 48.2% of subjects who had not been vaccinated, and they had a lower median age compared to the vaccinated subjects (47 vs. 61 years). An increasing number of infections in the vaccinated subjects were observed over time, with the highest proportion in November (85.2%). The variants correlated with clinical status; the largest proportion of symptomatic patients (59.6%) was observed with the Delta variant, while subjects harbouring the Gamma variant showed the highest proportion of asymptomatic infection (21.6%), albeit also deaths (5.4%). The Omicron variant was only found in the vaccinated subjects, of which 47% had been hospitalised. The diffusivity and pathogenicity associated with the different SARS-CoV-2 variants are likely to have relevant public health implications, both at the national and international levels. Our study provides data on the rapid changes in the epidemiological landscape of the SARS-CoV-2 variants in Italy. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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12 pages, 2836 KiB

Open AccessArticle

Systematic Genomic Surveillance of SARS-CoV-2 Virus on Illumina Sequencing Platforms in the Slovak Republic—One Year Experience

by Diana Rusňáková, Tatiana Sedláčková, Peter Radvák, Miroslav Böhmer, Pavol Mišenko, Jaroslav Budiš, Silvia Bokorová, Nikola Lipková, Michaela Forgáčová-Jakúbková, Tomáš Sládeček, Jozef Sitarčík, Werner Krampl, Michaela Gažiová, Anna Kaliňáková, Edita Staroňová, Elena Tichá, Terézia Vrábľová, Lucia Ševčíková, Barbora Kotvasová, Lucia Maďarová, Soňa Feiková, Kristína Beňová, Lenka Reizigová, Zuzana Onderková, Dorota Ondrušková, Dušan Loderer, Mária Škereňová, Zuzana Danková, Katarína Janíková, Erika Halašová, Elena Nováková, Ján Turňa and Tomáš Szemes Show full author list Hide full author list

Viruses 2022, 14(11), 2432; https://doi.org/10.3390/v14112432 - 2 Nov 2022

Cited by 10 | Viewed by 3023

Abstract

To explore a genomic pool of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the pandemic, the Ministry of Health of the Slovak Republic formed a genomics surveillance workgroup, and the Public Health Authority of the Slovak Republic launched a systematic national epidemiological [...] Read more.

To explore a genomic pool of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the pandemic, the Ministry of Health of the Slovak Republic formed a genomics surveillance workgroup, and the Public Health Authority of the Slovak Republic launched a systematic national epidemiological surveillance using whole-genome sequencing (WGS). Six out of seven genomic centers implementing Illumina sequencing technology were involved in the national SARS-CoV-2 virus sequencing program. Here we analyze a total of 33,024 SARS-CoV-2 isolates collected from the Slovak population from 1 March 2021, to 31 March 2022, that were sequenced and analyzed in a consistent manner. Overall, 28,005 out of 30,793 successfully sequenced samples met the criteria to be deposited in the global GISAID database. During this period, we identified four variants of concern (VOC)—Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529). In detail, we observed 165 lineages in our dataset, with dominating Alpha, Delta and Omicron in three major consecutive incidence waves. This study aims to describe the results of a routine but high-level SARS-CoV-2 genomic surveillance program. Our study of SARS-CoV-2 genomes in collaboration with the Public Health Authority of the Slovak Republic also helped to inform the public about the epidemiological situation during the pandemic. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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16 pages, 1377 KiB

Open AccessArticle

Retrospective Analysis of the SARS-CoV-2 Infection Profile in COVID-19 Positive Patients in Vitoria da Conquista, Northeast Brazil

by Anna Carolina S. Dantas, Hellen B. M. Oliveira, Camila P. Gomes, Daniele L. Alves, Priscilla D. B. Infante, Rosimara de J. A. Caitité, Hegger M. Fritsch, Marina S. Cucco, Lucas S. C. Silva, Caline N. T. Oliveira, Rafaela de S. Bittencourt, Aline T. Amorim, Ana Luisa P. Nascimento, Francely A. G. C. Marinho, Danielle S. de Medeiros, Márcio G. G. de Oliveira, Sostenes Mistro, Fabricio F. de Melo, Taiana T. S. Pereira, Ana M. S. Guimarães, Jorge Timenetsky, Pablo Maciel B. Moreira, Sandra Helena P. de Oliveira, Luiz C. J. Alcantara, Marta Giovanetti, Luciane A. Santos, Vagner Fonseca, Fernanda K. Barreto, Guilherme B. Campos and Lucas M. Marques Show full author list Hide full author list

Viruses 2022, 14(11), 2424; https://doi.org/10.3390/v14112424 - 31 Oct 2022

Cited by 3 | Viewed by 3146

Abstract

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for causing Coronavirus Disease-2019 (COVID-19), a heterogeneous clinical condition that manifests varying symptom severity according to the demographic profile of the studied population. While many studies have focused on the spread of COVID-19 in large [...] Read more.

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for causing Coronavirus Disease-2019 (COVID-19), a heterogeneous clinical condition that manifests varying symptom severity according to the demographic profile of the studied population. While many studies have focused on the spread of COVID-19 in large urban centers in Brazil, few have evaluated medium or small cities in the Northeast region. The aims of this study were: (i) to identify risk factors for mortality from SARS-CoV-2 infection, (ii) to evaluate the gene expression patterns of key immune response pathways using nasopharyngeal swabs of COVID-19 patients, and (iii) to identify the circulating SARS-CoV-2 variants in the residents of a medium-sized city in Northeast Brazil. A total of 783 patients infected with SARS-CoV-2 between May 2020 and August 2021 were included in this study. Clinical-epidemiological data from patients who died and those who survived were compared. Patients were also retrospectively divided into three groups based on disease severity: asymptomatic, mild, and moderate/severe. Samples were added to a qPCR array for analyses of 84 genes involved with immune response pathways and sequenced using the Oxford Nanopore MinION technology. Having pre-existing comorbidity; being male; having cardiovascular disease, diabetes, and/or chronic obstructive pulmonary disease; and PCR cycle threshold (Ct) values under 22 were identified as risk factors for mortality. Analysis of the expression profiles of inflammatory pathway genes showed that the greater the infection severity, the greater the activation of inflammatory pathways, triggering the cytokine storm and downregulating anti-inflammatory pathways. Viral genome analysis revealed the circulation of multiple lineages, such as B.1, B.1.1.28, Alpha, and Gamma, suggesting that multiple introduction events had occurred over time. This study’s findings help identify the specific strains and increase our understanding of the true state of local health. In addition, our data demonstrate that epidemiological and genomic surveillance together can help formulate public health strategies to guide governmental actions. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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12 pages, 1722 KiB

Open AccessArticle

SARS-CoV-2 from COVID-19 Patients in the Republic of Moldova: Whole-Genome Sequencing Results

by Alexandr Morozov, Vadim Nirca, Anna Victorova, Sven Poppert, Hagen Frickmann, Chiaki Yamada, Melissa A. Kacena, Sergiu Rata and Alexandru Movila

Viruses 2022, 14(10), 2310; https://doi.org/10.3390/v14102310 - 21 Oct 2022

Cited by 3 | Viewed by 2320

Abstract

Since the onset of the COVID-19 pandemic, no viral genome sequences of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have been documented from the Republic of Moldova, a developing country geographically located in Eastern Europe between Romania and Ukraine. Here, we report the [...] Read more.

Since the onset of the COVID-19 pandemic, no viral genome sequences of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have been documented from the Republic of Moldova, a developing country geographically located in Eastern Europe between Romania and Ukraine. Here, we report the analysis of 96 SARS-CoV-2 sequences from Delta and Omicron variants of the SARS-CoV-2 cases in the Republic of Moldova obtained between August and November 2021 and between January and May 2022. Comparison to global viral sequences showed that among the Delta variant of the SARS-CoV-2, AY.122 (n = 25), followed by AY.4.2.3 (n = 6), AY.4 (n = 5), AY.43 (n = 3), AY.98.1 (n = 3), B.1.617.2 (n = 1), AY.125 (n = 1), AY.54 (n = 1), AY.9 (n = 1), AY.126 (n = 1), and AY.33 (n = 1) were the most frequently found lineages. Furthermore, 10 lineages of the Omicron variant, namely, BA.2 (n = 14), followed by BA.2.9 (n = 10), BA.1 (n = 5), BA.1.1 (n = 5), BA.1.18 (n = 4), BA.1.15.1 (n = 3), BA.1.17.2 (n = 2), BA.1.17 (n = 2), BA.1.15 (n = 1), and BA.2.1 (n = 1) were detected. In addition, we also identified the impact of the military crisis between Russia and Ukraine, when the COVID-19 epidemiological rules collapsed, on the distribution of Delta and Omicron variants in the Republic of Moldova. Additional studies are warranted to characterize further the impact of the war between Russia and Ukraine on the genomic epidemiology of the SARS-CoV-2 in the Republic of Moldova and Eastern Europe. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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12 pages, 2256 KiB

Open AccessArticle

Dynamics of SARS-CoV-2 Variants of Concern in Vaccination Model City in the State of Sao Paulo, Brazil

by Svetoslav Nanev Slavov, Debora Glenda Lima de La-Roque, Pericles Natan Mendes da Costa, Evandra Strazza Rodrigues, Elaine Vieira Santos, Josiane Serrano Borges, Mariane Evaristo, Juliana de Matos Maçonetto, Adriana Aparecida Marques, Jonathan Milhomens, Felipe Augusto Rós, Vagner Fonseca, Alex Ranieri Jerônimo Lima, Gabriela Ribeiro, Loyze Paola Oliveira de Lima, Pedro Manuel Marques Garibaldi, Natasha Nicos Ferreira, Glenda Renata Moraes, Elaine Cristina Marqueze, Claudia Renata dos Santos Barros, Antonio Jorge Martins, Luiz Lehmann Coutinho, Rodrigo Tocantins Calado, Marcos Borges, Maria Carolina Elias, Sandra Coccuzzo Sampaio, Marta Giovanetti, Luiz Carlos Junior Alcantara, Dimas Tadeu Covas and Simone Kashima Show full author list Hide full author list

Viruses 2022, 14(10), 2148; https://doi.org/10.3390/v14102148 - 29 Sep 2022

Cited by 7 | Viewed by 4177

Abstract

From a country with one of the highest SARS-CoV-2 morbidity and mortality rates, Brazil has implemented one of the most successful vaccination programs. Brazil’s first model city vaccination program was performed by the CoronaVac vaccine (Sinovac Biotech) in the town of Serrana, São [...] Read more.

From a country with one of the highest SARS-CoV-2 morbidity and mortality rates, Brazil has implemented one of the most successful vaccination programs. Brazil’s first model city vaccination program was performed by the CoronaVac vaccine (Sinovac Biotech) in the town of Serrana, São Paulo State. To evaluate the vaccination effect on the SARS-CoV-2 molecular dynamics and clinical outcomes, we performed SARS-CoV-2 molecular surveillance on 4375 complete genomes obtained between June 2020 and April 2022 in this location. This study included the period between the initial SARS-CoV-2 introduction and during the vaccination process. We observed that the SARS-CoV-2 substitution dynamics in Serrana followed the viral molecular epidemiology in Brazil, including the initial identification of the ancestral lineages (B.1.1.28 and B.1.1.33) and epidemic waves of variants of concern (VOC) including the Gamma, Delta, and, more recently, Omicron. Most probably, as a result of the immunization campaign, the mortality during the Gamma and Delta VOC was significantly reduced compared to the rest of Brazil, which was also related to lower morbidity. Our phylogenetic analysis revealed the evolutionary history of the SARS-CoV-2 in this location and showed that multiple introduction events have occurred over time. The evaluation of the COVID-19 clinical outcome revealed that most cases were mild (88.9%, 98.1%, 99.1% to Gamma, Delta, and Omicron, respectively) regardless of the infecting VOC. In conclusion, we observed that vaccination was responsible for reducing the death toll rate and related COVID-19 morbidity, especially during the gamma and Delta VOC; however, it does not prevent the rapid substitution rate and morbidity of the Omicron VOC. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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18 pages, 3315 KiB

Open AccessArticle

Molecular Analyses of Clinical Isolates and Recombinant SARS-CoV-2 Carrying B.1 and B.1.617.2 Spike Mutations Suggest a Potential Role of Non-Spike Mutations in Infection Kinetics

by Andrei Veleanu, Maximilian A. Kelch, Chengjin Ye, Melanie Flohr, Alexander Wilhelm, Marek Widera, Luis Martinez-Sobrido, Sandra Ciesek and Tuna Toptan

Viruses 2022, 14(9), 2017; https://doi.org/10.3390/v14092017 - 12 Sep 2022

Cited by 3 | Viewed by 3509

Abstract

Some of the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are less susceptible to neutralization with post-vaccine sera and monoclonal antibodies targeting the viral spike glycoprotein. This raises concerns of disease control, transmissibility, and severity. Numerous substitutions have been identified to [...] Read more.

Some of the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are less susceptible to neutralization with post-vaccine sera and monoclonal antibodies targeting the viral spike glycoprotein. This raises concerns of disease control, transmissibility, and severity. Numerous substitutions have been identified to increase viral fitness within the nucleocapsid and nonstructural proteins, in addition to spike mutations. Therefore, we sought to generate infectious viruses carrying only the variant-specific spike mutations in an identical backbone to evaluate the impact of spike and non-spike mutations in the virus life cycle. We used en passant mutagenesis to generate recombinant viruses carrying spike mutations of B.1 and B.1.617.2 variants using SARS-CoV-2- bacterial artificial chromosome (BAC). Neutralization assays using clinical sera yielded comparable results between recombinant viruses and corresponding clinical isolates. Non-spike mutations for both variants neither seemed to effect neutralization efficiencies with monoclonal antibodies nor the response to treatment with inhibitors. However, live-cell imaging and microscopy revealed differences, such as persisting syncytia and pronounced cytopathic effect formation, as well as their progression between BAC-derived viruses and clinical isolates in human lung epithelial cell lines and primary bronchial epithelial cells. Complementary RNA analyses further suggested a potential role of non-spike mutations in infection kinetics. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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15 pages, 2119 KiB

Open AccessArticle

Early Detection of SARS-CoV-2 Omicron BA.4 and BA.5 in German Wastewater

by Alexander Wilhelm, Shelesh Agrawal, Jens Schoth, Christina Meinert-Berning, Daniel Bastian, Laura Orschler, Sandra Ciesek, Burkhard Teichgräber, Thomas Wintgens, Susanne Lackner, Frank-Andreas Weber and Marek Widera

Viruses 2022, 14(9), 1876; https://doi.org/10.3390/v14091876 - 25 Aug 2022

Cited by 17 | Viewed by 3295

Abstract

Wastewater-based SARS-CoV-2 epidemiology (WBE) has been established as an important tool to support individual testing strategies. The Omicron sub-variants BA.4/BA.5 have spread globally, displacing the preceding variants. Due to the severe transmissibility and immune escape potential of BA.4/BA.5, early monitoring was required to [...] Read more.

Wastewater-based SARS-CoV-2 epidemiology (WBE) has been established as an important tool to support individual testing strategies. The Omicron sub-variants BA.4/BA.5 have spread globally, displacing the preceding variants. Due to the severe transmissibility and immune escape potential of BA.4/BA.5, early monitoring was required to assess and implement countermeasures in time. In this study, we monitored the prevalence of SARS-CoV-2 BA.4/BA.5 at six municipal wastewater treatment plants (WWTPs) in the Federal State of North Rhine-Westphalia (NRW, Germany) in May and June 2022. Initially, L452R-specific primers/probes originally designed for SARS-CoV-2 Delta detection were validated using inactivated authentic viruses and evaluated for their suitability for detecting BA.4/BA.5. Subsequently, the assay was used for RT-qPCR analysis of RNA purified from wastewater obtained twice a week at six WWTPs. The occurrence of L452R carrying RNA was detected in early May 2022, and the presence of BA.4/BA.5 was confirmed by variant-specific single nucleotide polymorphism PCR (SNP-PCR) targeting E484A/F486V and NGS sequencing. Finally, the mutant fractions were quantitatively monitored by digital PCR, confirming BA.4/BA.5 as the majority variant by 5 June 2022. In conclusion, the successive workflow using RT-qPCR, variant-specific SNP-PCR, and RT-dPCR demonstrates the strength of WBE as a versatile tool to rapidly monitor variants spreading independently of individual test capacities. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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17 pages, 1532 KiB

Open AccessArticle

Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern

by Ben Katowa, Annie Kalonda, Benjamin Mubemba, Japhet Matoba, Doreen Mainza Shempela, Jay Sikalima, Boniface Kabungo, Katendi Changula, Simbarashe Chitanga, Mpanga Kasonde, Otridah Kapona, Nathan Kapata, Kunda Musonda, Mwaka Monze, John Tembo, Matthew Bates, Alimuddin Zumla, Catherine G. Sutcliffe, Masahiro Kajihara, Junya Yamagishi, Ayato Takada, Hirofumi Sawa, Roma Chilengi, Victor Mukonka, Walter Muleya and Edgar Simulundu Show full author list Hide full author list

Viruses 2022, 14(9), 1865; https://doi.org/10.3390/v14091865 - 24 Aug 2022

Cited by 4 | Viewed by 3665

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares international [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares international borders with Botswana, Namibia, and Zimbabwe and is a major tourist destination. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116), and multiple Omicron subvariants with the BA.1 subvariant being predominant. Whereas Beta, Delta, and Omicron variants were associated with the second, third, and fourth pandemic waves, respectively, the Alpha variant was not associated with any wave in the country. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Zambia from different European and African countries. Across the 40 genomes analysed, a total of 292 mutations were observed, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. This study stresses the need for the continued monitoring of SARS-CoV-2 circulation in Zambia, particularly in strategically positioned regions such as the Southern Province which could be at increased risk of introduction of novel VOCs. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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8 pages, 247 KiB

Open AccessArticle

Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2

by David Pham, Susan Maddocks, Dominic E. Dwyer, Vitali Sintchenko, Jen Kok and Rebecca J. Rockett

Viruses 2022, 14(8), 1760; https://doi.org/10.3390/v14081760 - 12 Aug 2022

Cited by 1 | Viewed by 1928

Abstract

In order to rapidly differentiate sublineages BA.1 and BA.2 of the SARS-CoV-2 variant of concern Omicron, we developed a real-time reverse-transcriptase polymerase chain reaction to target the discriminatory spike protein deletion at amino acid position 69–70 (S:del69–70). Compared to the gold standard of [...] Read more.

In order to rapidly differentiate sublineages BA.1 and BA.2 of the SARS-CoV-2 variant of concern Omicron, we developed a real-time reverse-transcriptase polymerase chain reaction to target the discriminatory spike protein deletion at amino acid position 69–70 (S:del69–70). Compared to the gold standard of whole genome sequencing, the candidate assay was 100% sensitive and 99.4% specific. Sublineage typing by RT-PCR can provide a rapid, high throughput and cost-effective method to enhance surveillance as well as potentially guiding treatment and infection control decisions. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

17 pages, 3438 KiB

Open AccessArticle

Dynamics and Determinants of SARS-CoV-2 RT-PCR Testing on Symptomatic Individuals Attending Healthcare Centers during 2020 in Bahia, Brazil

by Felicidade Mota Pereira, Aline Salomão de Araujo, Ana Catarina Martins Reis, Anadilton Santos da Hora, Francesco Pinotti, Robert S. Paton, Camylla Vilas Boas Figueiredo, Caroline Lopes Damasceno, Daiana Carlos dos Santos, Daniele Souza de Santana, Danielle Freitas Sales, Evelyn Ariana Andrade Brandão, Everton da Silva Batista, Fulvia Soares Campos de Sousa, Gabriela Santana Menezes, Jackeline Silveira dos Santos, Jaqueline Gomes Lima, Jean Tadeu Brito, Lenisa Dandara dos Santos, Luciana Reboredo, Maiara Santana Santos, Marcela Kelly Astete Gomez, Marcia Freitas da Cruz, Mariana Rosa Ampuero, Mariele Guerra Lemos da Silva, Mariza S. da Paixão Melo, Marta Ferreira da Silva, Nadja de Jesus Gonçalves dos Santos, Núbia de Souza Pessoa, Ramile Silva de Araujo, Taiane de Macedo Godim, Stephane Fraga de Oliveira Tosta, Vanessa Brandão Nardy, Elaine Cristina Faria, Breno Frederico de Carvalho Dominguez Souza, Jessica Laís Almeida dos Santos, Paul Wikramaratna, Marta Giovanetti, Luiz Carlos Junior Alcântara, José Lourenço and Arabela Leal e Silva de Mello Show full author list Hide full author list

Viruses 2022, 14(7), 1549; https://doi.org/10.3390/v14071549 - 15 Jul 2022

Cited by 2 | Viewed by 2785

Abstract

RT-PCR testing data provides opportunities to explore regional and individual determinants of test positivity and surveillance infrastructure. Using Generalized Additive Models, we explored 222,515 tests of a random sample of individuals with COVID-19 compatible symptoms in the Brazilian state of Bahia during 2020. [...] Read more.

RT-PCR testing data provides opportunities to explore regional and individual determinants of test positivity and surveillance infrastructure. Using Generalized Additive Models, we explored 222,515 tests of a random sample of individuals with COVID-19 compatible symptoms in the Brazilian state of Bahia during 2020. We found that age and male gender were the most significant determinants of test positivity. There was evidence of an unequal impact among socio-demographic strata, with higher positivity among those living in areas with low education levels during the first epidemic wave, followed by those living in areas with higher education levels in the second wave. Our estimated probability of testing positive after symptom onset corroborates previous reports that the probability decreases with time, more than halving by about two weeks and converging to zero by three weeks. Test positivity rates generally followed state-level reported cases, and while a single laboratory performed ~90% of tests covering ~99% of the state’s area, test turn-around time generally remained below four days. This testing effort is a testimony to the Bahian surveillance capacity during public health emergencies, as previously witnessed during the recent Zika and Yellow Fever outbreaks. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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14 pages, 2301 KiB

Open AccessArticle

Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico

by Blanca Taboada, Selene Zárate, Rodrigo García-López, José Esteban Muñoz-Medina, Alejandro Sanchez-Flores, Alfredo Herrera-Estrella, Celia Boukadida, Bruno Gómez-Gil, Nelly Selem Mojica, Mauricio Rosales-Rivera, Angel Gustavo Salas-Lais, Rosa María Gutiérrez-Ríos, Antonio Loza, Xaira Rivera-Gutierrez, Joel Armando Vazquez-Perez, Margarita Matías-Florentino, Marissa Pérez-García, Santiago Ávila-Ríos, Juan Manuel Hurtado, Carla Ivón Herrera-Nájera, José de Jesús Núñez-Contreras, Brenda Sarquiz-Martínez, Víctor Eduardo García-Arias, María Guadalupe Santiago-Mauricio, Bernardo Martínez-Miguel, Julissa Enciso-Ibarra, Cristóbal Cháidez-Quiróz, Pavel Iša, Rosa María Wong-Chew, María-Eugenia Jiménez-Corona, Susana López and Carlos F. Arias Show full author list Hide full author list

Viruses 2022, 14(6), 1165; https://doi.org/10.3390/v14061165 - 27 May 2022

Cited by 15 | Viewed by 4429

Abstract

In this study, we analyzed the sequences of SARS-CoV-2 isolates of the Delta variant in Mexico, which has completely replaced other previously circulating variants in the country due to its transmission advantage. Among all the Delta sublineages that were detected, 81.5 % were [...] Read more.

In this study, we analyzed the sequences of SARS-CoV-2 isolates of the Delta variant in Mexico, which has completely replaced other previously circulating variants in the country due to its transmission advantage. Among all the Delta sublineages that were detected, 81.5 % were classified as AY.20, AY.26, and AY.100. According to publicly available data, these only reached a world prevalence of less than 1%, suggesting a possible Mexican origin. The signature mutations of these sublineages are described herein, and phylogenetic analyses and haplotype networks are used to track their spread across the country. Other frequently detected sublineages include AY.3, AY.62, AY.103, and AY.113. Over time, the main sublineages showed different geographical distributions, with AY.20 predominant in Central Mexico, AY.26 in the North, and AY.100 in the Northwest and South/Southeast. This work describes the circulation, from May to November 2021, of the primary sublineages of the Delta variant associated with the third wave of the COVID-19 pandemic in Mexico and highlights the importance of SARS-CoV-2 genomic surveillance for the timely identification of emerging variants that may impact public health. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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10 pages, 1781 KiB

Open AccessBrief Report

Unveiling the Impact of the Omicron Variant: Insights from Genomic Surveillance in Mato Grosso do Sul, Midwest Brazil

by Lívia de Mello Almeida Maziero, Marta Giovanetti, Vagner Fonseca, Marina Castilhos Souza Umaki Zardin, Gislene Garcia de Castro Lichs, Grazielli Rocha de Rezende Romera, Daniel Henrique Tsuha, Danila Fernanda Rodrigues Frias, Valdir Castanho Escandolhero, Luiz Henrique Demarchi, Larissa Domingues Castilho, Karine Ferreira Barbosa, Danielle Galindo Martins Tebet, Joilson Xavier, Hegger Fritsch, Mauricio Lima, Carla de Oliveira, Elaine Vieira Santos, Simone Kashima, Rodrigo Fabiano do Carmo Said, Alexander Rosewell, Julio Croda, Luiz Carlos Junior Alcantara and Crhistinne Cavalheiro Maymone Gonçalves Show full author list Hide full author list

Viruses 2023, 15(7), 1604; https://doi.org/10.3390/v15071604 - 22 Jul 2023

Cited by 3 | Viewed by 1693

Abstract

Genomic surveillance has emerged as a crucial tool in monitoring and understanding the dynamics of viral variants during the COVID-19 pandemic. In the Midwest region of Brazil, Mato Grosso do Sul has faced a significant burden from the SARS-CoV-2 epidemic, with a total [...] Read more.

Genomic surveillance has emerged as a crucial tool in monitoring and understanding the dynamics of viral variants during the COVID-19 pandemic. In the Midwest region of Brazil, Mato Grosso do Sul has faced a significant burden from the SARS-CoV-2 epidemic, with a total of 613,000 confirmed cases as of June 2023. In collaboration with the Central Public Health Laboratory in the capital city of Campo Grande, we conducted a portable whole-genome sequencing and phylodynamic analysis to investigate the circulation of the Omicron variant in the region. The study aimed to uncover the genomic landscape and provide valuable insights into the prevalence and transmission patterns of this highly transmissible variant. Our findings revealed an increase in the number of cases within the region during 2022, followed by a gradual decline as a result of the successful impact of the vaccination program together with the capacity of this unpredictable and very transmissible variant to quickly affect the proportion of susceptible population. Genomic data indicated multiple introduction events, suggesting that human mobility played a differential role in the variant’s dispersion dynamics throughout the state. These findings emphasize the significance of implementing public health interventions to mitigate further spread and highlight the powerful role of genomic monitoring in promptly tracking and uncovering the circulation of viral strains. Together those results underscore the importance of proactive surveillance, rapid genomic sequencing, and data sharing to facilitate timely public health responses. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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15 pages, 5744 KiB

Open AccessSystematic Review

SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis

by Diego Menezes, Paula Luize Camargos Fonseca, João Locke Ferreira de Araújo and Renan Pedra de Souza

Viruses 2022, 14(12), 2715; https://doi.org/10.3390/v14122715 - 5 Dec 2022

Cited by 11 | Viewed by 3392

Abstract

Several studies have monitored the SARS-CoV-2 variants in Brazil throughout the pandemic. Here, we systematically reviewed and conducted a scientometric analysis of the SARS-CoV-2 genomic surveillance studies using Brazilian samples. A Pubmed database search on October 2022 returned 492 articles, of which 106 [...] Read more.

Several studies have monitored the SARS-CoV-2 variants in Brazil throughout the pandemic. Here, we systematically reviewed and conducted a scientometric analysis of the SARS-CoV-2 genomic surveillance studies using Brazilian samples. A Pubmed database search on October 2022 returned 492 articles, of which 106 were included. Ninety-six different strains were reported, with variant of concern (VOC) gamma (n = 35,398), VOC delta (n = 15,780), and the variant of interest zeta (n = 1983) being the most common. The top three states with the most samples in the published articles were São Paulo, Rio de Janeiro, and Minas Gerais. Whereas the first year of the pandemic presented primary circulation of B.1.1.28 and B.1.1.33 variants, consecutive replacements were observed between them and VOI zeta, VOC gamma, VOC delta, and VOC omicron. VOI mu, VOI lambda, VOC alpha, and VOC beta were also detected but failed to reach significant circulation. Co-infection, re-infection, and vaccine breakthrough reports were found. Article co-citation differed from the co-authorship structure. Despite the limitations, we expect to give an overview of Brazil’s genomic surveillance studies and contribute to future research execution. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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6 pages, 491 KiB

Open AccessCommentary

Evolution of SARS-CoV-2: BA.4/BA.5 Variants Continues to Pose New Challenges

by Neha Quadir, Jasdeep Singh, Anwar Alam, Asrar Ahmad Malik, Syed Asad Rahman, Subhash Hira, Nasreen Zafar Ehtesham, Durai Sundar and Seyed Ehtesham Hasnain

Viruses 2022, 14(12), 2610; https://doi.org/10.3390/v14122610 - 23 Nov 2022

Cited by 9 | Viewed by 2246

Abstract

The acquisition of a high number of mutations, notably, the gain of two mutations L452R and F486V in RBD, and the ability to evade vaccine/natural infection-induced immunity suggests that Omicron is continuing to use “immune-escape potential” as an evolutionary space to maintain a [...] Read more.

The acquisition of a high number of mutations, notably, the gain of two mutations L452R and F486V in RBD, and the ability to evade vaccine/natural infection-induced immunity suggests that Omicron is continuing to use “immune-escape potential” as an evolutionary space to maintain a selection advantage within the population. Despite the low hospitalizations and lower death rate, the surges by these variants may offset public health measures and disrupt health care facilities as seen recently in Portugal and the USA. Interestingly these BA.4/BA.5 variants have been found to be more severe than the earlier-emerged Omicron variants. We believe that aggressive COVID-19 surveillance using affordable testing strategies might actually help understand the evolution and transmission pattern of new variants. The sudden dip in reporting of new cases in some of the low- and middle-income countries is an alarming situation and needs to be addressed as this could lead to undetected transmission of future variants of interest/concern of SARS-CoV-2 in large population settings, including advent of a ‘super’ virus. It would be interesting to examine the possible role/influence, if any, of the two different kinds of vaccines, the spike protein-based versus the inactivated whole virus, in the evolution of BA.4/BA.5. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2)

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