Viruses

Editorial

Jump to: Research, Review, Other

6 pages, 229 KiB

Open AccessEditorial

Special Issue “Viral Infections in Developing Countries”

by Fabrício Souza Campos, Luciana Barros de Arruda and Flávio Guimaraes da Fonseca

Viruses 2022, 14(2), 405; https://doi.org/10.3390/v14020405 - 16 Feb 2022

Cited by 4 | Viewed by 1810

Abstract

Viral infections by endemic, emerging, and reemerging viruses are constantly challenging public health systems and health policies all over the world [...] Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

Research

Jump to: Editorial, Review, Other

14 pages, 726 KiB

Open AccessArticle

High Level of Pre-Treatment HIV-1 Drug Resistance and Its Association with HLA Class I-Mediated Restriction in the Pumwani Sex Worker Cohort

by Rachel Willim, Elnaz Shadabi, Raghavan Sampathkumar, Lin Li, Robert Balshaw, Joshua Kimani, Francis A. Plummer, Ma Luo and Binhua Liang

Viruses 2022, 14(2), 273; https://doi.org/10.3390/v14020273 - 28 Jan 2022

Cited by 4 | Viewed by 2548

Abstract

Background: We analyzed the prevalence of pre-antiretroviral therapy (ART) drug resistance mutations (DRMs) in a Kenyan population. We also examined whether host HLA class I genes influence the development of pre-ART DRMs. Methods: The HIV-1 proviral DNAs were amplified from blood samples of [...] Read more.

Background: We analyzed the prevalence of pre-antiretroviral therapy (ART) drug resistance mutations (DRMs) in a Kenyan population. We also examined whether host HLA class I genes influence the development of pre-ART DRMs. Methods: The HIV-1 proviral DNAs were amplified from blood samples of 266 ART-naïve women from the Pumwani Sex Worker cohort of Nairobi, Kenya using a nested PCR method. The amplified HIV genomes were sequenced using next-generation sequencing technology. The prevalence of pre-ART DRMs was investigated. Correlation studies were performed between HLA class I alleles and HIV-1 DRMs. Results: Ninety-eight percent of participants had at least one DRM, while 38% had at least one WHO surveillance DRM. M184I was the most prevalent clinically important variant, seen in 37% of participants. The DRMs conferring resistance to one or more integrase strand transfer inhibitors were also found in up to 10% of participants. Eighteen potentially relevant (p < 0.05) positive correlations were found between HLA class 1 alleles and HIV drug-resistant variants. Conclusions: High levels of HIV drug resistance were found in all classes of antiretroviral drugs included in the current first-line ART regimens in Africa. The development of DRMs may be influenced by host HLA class I-restricted immunity. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

12 pages, 2130 KiB

Open AccessArticle

Could Phylogenetic Analysis Be Used for Feline Leukemia Virus (FeLV) Classification?

by Lucía Cano-Ortiz, Caroline Tochetto, Paulo Michel Roehe, Ana Cláudia Franco and Dennis Maletich Junqueira

Viruses 2022, 14(2), 249; https://doi.org/10.3390/v14020249 - 26 Jan 2022

Cited by 4 | Viewed by 2778

Abstract

The surface envelope (SU) protein determines the cell tropism and consequently the pathogenesis of the feline leukemia virus (FeLV) in felids. Recombination of exogenous FeLV (exFeLV) with endogenous retroviruses (enFeLV) allows the emergence of more pathogenic variants. Currently, phenotypic testing through interference assays [...] Read more.

The surface envelope (SU) protein determines the cell tropism and consequently the pathogenesis of the feline leukemia virus (FeLV) in felids. Recombination of exogenous FeLV (exFeLV) with endogenous retroviruses (enFeLV) allows the emergence of more pathogenic variants. Currently, phenotypic testing through interference assays is the only method to distinguish among subgroups—namely, FeLV-A, -B, -C, -E, and -T. This study proposes a new method for FeLV classification based on molecular analysis of the SU gene. A total of 404 publicly available SU sequences were used to reconstruct a maximum likelihood tree. However, only 63 of these sequences had available information about phenotypic tests or subgroup assignments. Two major clusters were observed: (a) clade FeLV-A, which includes FeLV-A, FeLV-C, FeLV-E, and FeLV-T sequences, and (b) clade enFeLV, which includes FeLV-B and enFeLV strains. We found that FeLV-B, FeLV-C, FeLV-E, and FeLV-T SU sequences share similarities to FeLV-A viruses and most likely arose independently through mutation or recombination from this strain. FeLV-B and FeLV-C arose from recombination between FeLV-A and enFeLV viruses, whereas FeLV-T is a monophyletic subgroup that has probably originated from FeLV-A through combined events of deletions and insertions. Unfortunately, this study could not identify polymorphisms that are specifically linked to the FeLV-E subgroup. We propose that phylogenetic and recombination analysis together can explain the current phenotypic classification of FeLV viruses. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

16 pages, 1123 KiB

Open AccessArticle

Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020—March 2021) Using a Statistical Learning Strategy

by Lue Ping Zhao, Terry P. Lybrand, Peter B. Gilbert, Thomas R. Hawn, Joshua T. Schiffer, Leonidas Stamatatos, Thomas H. Payne, Lindsay N. Carpp, Daniel E. Geraghty and Keith R. Jerome

Viruses 2022, 14(1), 9; https://doi.org/10.3390/v14010009 - 21 Dec 2021

Cited by 13 | Viewed by 3446

Abstract

The emergence and establishment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of interest (VOIs) and variants of concern (VOCs) highlight the importance of genomic surveillance. We propose a statistical learning strategy (SLS) for identifying and spatiotemporally tracking potentially relevant Spike protein [...] Read more.

The emergence and establishment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of interest (VOIs) and variants of concern (VOCs) highlight the importance of genomic surveillance. We propose a statistical learning strategy (SLS) for identifying and spatiotemporally tracking potentially relevant Spike protein mutations. We analyzed 167,893 Spike protein sequences from coronavirus disease 2019 (COVID-19) cases in the United States (excluding 21,391 sequences from VOI/VOC strains) deposited at GISAID from 19 January 2020 to 15 March 2021. Alignment against the reference Spike protein sequence led to the identification of viral residue variants (VRVs), i.e., residues harboring a substitution compared to the reference strain. Next, generalized additive models were applied to model VRV temporal dynamics and to identify VRVs with significant and substantial dynamics (false discovery rate q-value < 0.01; maximum VRV proportion >10% on at least one day). Unsupervised learning was then applied to hierarchically organize VRVs by spatiotemporal patterns and identify VRV-haplotypes. Finally, homology modeling was performed to gain insight into the potential impact of VRVs on Spike protein structure. We identified 90 VRVs, 71 of which had not previously been observed in a VOI/VOC, and 35 of which have emerged recently and are durably present. Our analysis identified 17 VRVs ~91 days earlier than their first corresponding VOI/VOC publication. Unsupervised learning revealed eight VRV-haplotypes of four VRVs or more, suggesting two emerging strains (B1.1.222 and B.1.234). Structural modeling supported a potential functional impact of the D1118H and L452R mutations. The SLS approach equally monitors all Spike residues over time, independently of existing phylogenic classifications, and is complementary to existing genomic surveillance methods. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

12 pages, 3959 KiB

Open AccessArticle

Establishment of Outbreak Thresholds for Hepatitis A in South Africa Using Laboratory Surveillance, 2017–2020

by Nishi Prabdial-Sing, Villyen Motaze, Jack Manamela, Kerrigan McCarthy and Melinda Suchard

Viruses 2021, 13(12), 2470; https://doi.org/10.3390/v13122470 - 10 Dec 2021

Cited by 7 | Viewed by 2927

Abstract

As South Africa transitions from endemic to intermediate endemicity, hepatitis A surveillance needs strengthening to monitor trends in disease incidence and to identify outbreaks. We used passive laboratory-based surveillance data from the National Health Laboratory Services to calculate national hepatitis A incidence and [...] Read more.

As South Africa transitions from endemic to intermediate endemicity, hepatitis A surveillance needs strengthening to monitor trends in disease incidence and to identify outbreaks. We used passive laboratory-based surveillance data from the National Health Laboratory Services to calculate national hepatitis A incidence and to establish thresholds for outbreaks. Incidence was calculated by age and geographic location. The static threshold used two or three standard deviations (SDs) above the mean hepatitis A incidence in 2017–2019, and a cumulative summation (CuSum2) threshold used three SDs above the mean of the preceding seven months. These thresholds were applied to hepatitis A data for 2020. From 2017 to 2020, the mean incidence of hepatitis A IgM was 4.06/100,000 and ranged from 4.23 to 4.85/100,000 per year. Hepatitis A incidence was highest in the Western Cape province (WCP) (7.00–10.92/100,000 per year). The highest incidence was in the 1–9-year-olds. The incidence of hepatitis A in 2020 exceeded the static threshold in two districts of the WCP: Cape Winelands in January and Overberg district in August. The provincial incidence did not exceed the static and CuSum2 thresholds. District-level analysis using either threshold was sensitive enough to monitor trends and to alert district health authorities, allowing early outbreak responses. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

17 pages, 3521 KiB

Open AccessArticle

The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City

by Alberto Cedro-Tanda, Laura Gómez-Romero, Nicolás Alcaraz, Guillermo de Anda-Jauregui, Fernando Peñaloza, Bernardo Moreno, Marco A. Escobar-Arrazola, Oscar A. Ramirez-Vega, Paulina Munguia-Garza, Francisco Garcia-Cardenas, Mireya Cisneros-Villanueva, Jose L. Moreno-Camacho, Jorge Rodriguez-Gallegos, Marco A. Luna-Ruiz Esparza, Miguel A. Fernández Rojas, Alfredo Mendoza-Vargas, Juan Pablo Reyes-Grajeda, Abraham Campos-Romero, Ofelia Angulo, Rosaura Ruiz, Claudia Sheinbaum-Pardo, José Sifuentes-Osornio, David Kershenobich, Alfredo Hidalgo-Miranda and Luis A. Herrera Show full author list Hide full author list

Viruses 2021, 13(11), 2182; https://doi.org/10.3390/v13112182 - 29 Oct 2021

Cited by 26 | Viewed by 6423

Abstract

The SARS-CoV-2 pandemic is one of the most concerning health problems around the globe. We reported the emergence of SARS-CoV-2 variant B.1.1.519 in Mexico City. We reported the effective reproduction number (Rt) of B.1.1.519 and presented evidence of its geographical origin based on [...] Read more.

The SARS-CoV-2 pandemic is one of the most concerning health problems around the globe. We reported the emergence of SARS-CoV-2 variant B.1.1.519 in Mexico City. We reported the effective reproduction number (Rt) of B.1.1.519 and presented evidence of its geographical origin based on phylogenetic analysis. We also studied its evolution via haplotype analysis and identified the most recurrent haplotypes. Finally, we studied the clinical impact of B.1.1.519. The B.1.1.519 variant was predominant between November 2020 and May 2021, reaching 90% of all cases sequenced in February 2021. It is characterized by three amino acid changes in the spike protein: T478K, P681H, and T732A. Its Rt varies between 0.5 and 2.9. Its geographical origin remain to be investigated. Patients infected with variant B.1.1.519 showed a highly significant adjusted odds ratio (aOR) increase of 1.85 over non-B.1.1.519 patients for developing a severe/critical outcome (p = 0.000296, 1.33–2.6 95% CI) and a 2.35-fold increase for hospitalization (p = 0.005, 1.32–4.34 95% CI). The continuous monitoring of this and other variants will be required to control the ongoing pandemic as it evolves. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

16 pages, 2125 KiB

Open AccessArticle

A Multidisciplinary Investigation of the First Chikungunya Virus Outbreak in Matadi in the Democratic Republic of the Congo

by Anja De Weggheleire, Antoine Nkuba-Ndaye, Placide Mbala-Kingebeni, Joachim Mariën, Esaie Kindombe-Luzolo, Gillon Ilombe, Donatien Mangala-Sonzi, Guillaume Binene-Mbuka, Birgit De Smet, Florian Vogt, Philippe Selhorst, Mathy Matungala-Pafubel, Frida Nkawa, Fabien Vulu, Mathias Mossoko, Elisabeth Pukuta-Simbu, Eddy Kinganda-Lusamaki, Wim Van Bortel, Francis Wat’senga-Tezzo, Sheila Makiala-Mandanda and Steve Ahuka-Mundeke Show full author list Hide full author list

Viruses 2021, 13(10), 1988; https://doi.org/10.3390/v13101988 - 3 Oct 2021

Cited by 8 | Viewed by 3145

Abstract

Early March 2019, health authorities of Matadi in the Democratic Republic of the Congo alerted a sudden increase in acute fever/arthralgia cases, prompting an outbreak investigation. We collected surveillance data, clinical data, and laboratory specimens from clinical suspects (for CHIKV-PCR/ELISA, malaria RDT), semi-structured [...] Read more.

Early March 2019, health authorities of Matadi in the Democratic Republic of the Congo alerted a sudden increase in acute fever/arthralgia cases, prompting an outbreak investigation. We collected surveillance data, clinical data, and laboratory specimens from clinical suspects (for CHIKV-PCR/ELISA, malaria RDT), semi-structured interviews with patients/caregivers about perceptions and health seeking behavior, and mosquito sampling (adult/larvae) for CHIKV-PCR and estimation of infestation levels. The investigations confirmed a large CHIKV outbreak that lasted February–June 2019. The total caseload remained unknown due to a lack of systematic surveillance, but one of the two health zones of Matadi notified 2686 suspects. Of the clinical suspects we investigated (n = 220), 83.2% were CHIKV-PCR or IgM positive (acute infection). One patient had an isolated IgG-positive result (while PCR/IgM negative), suggestive of past infection. In total, 15% had acute CHIKV and malaria. Most adult mosquitoes and larvae (>95%) were Aedes albopictus. High infestation levels were noted. CHIKV was detected in 6/11 adult mosquito pools, and in 2/15 of the larvae pools. This latter and the fact that 2/6 of the CHIKV-positive adult pools contained only males suggests transovarial transmission. Interviews revealed that healthcare seeking shifted quickly toward the informal sector and self-medication. Caregivers reported difficulties to differentiate CHIKV, malaria, and other infectious diseases resulting in polypharmacy and high out-of-pocket expenditure. We confirmed a first major CHIKV outbreak in Matadi, with main vector Aedes albopictus. The health sector was ill-prepared for the information, surveillance, and treatment needs for such an explosive outbreak in a CHIKV-naïve population. Better surveillance systems (national level/sentinel sites) and point-of-care diagnostics for arboviruses are needed. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

12 pages, 2366 KiB

Open AccessArticle

Real-Time Genomic Surveillance during the 2021 Re-Emergence of the Yellow Fever Virus in Rio Grande do Sul State, Brazil

by Miguel de S. Andrade, Fabrício S. Campos, Aline A. S. Campos, Filipe V. S. Abreu, Fernando L. Melo, Anaiá da P. Sevá, Jader da C. Cardoso, Edmilson Dos Santos, Lucas C. Born, Cláudia M. D. da Silva, Nicolas F. D. Müller, Cirilo H. de Oliveira, Alex J. J. da Silva, Danilo Simonini-Teixeira, Sofía Bernal-Valle, Maria A. M. M. Mares-Guia, George R. Albuquerque, Alessandro P. M. Romano, Ana C. Franco, Bergmann M. Ribeiro, Paulo M. Roehe and Marco A. B. de Almeida Show full author list Hide full author list

Viruses 2021, 13(10), 1976; https://doi.org/10.3390/v13101976 - 1 Oct 2021

Cited by 20 | Viewed by 4103

Abstract

The 2021 re-emergence of yellow fever in non-human primates in the state of Rio Grande do Sul (RS), southernmost Brazil, resulted in the death of many howler monkeys (genus Alouatta) and led the state to declare a Public Health Emergency of State [...] Read more.

The 2021 re-emergence of yellow fever in non-human primates in the state of Rio Grande do Sul (RS), southernmost Brazil, resulted in the death of many howler monkeys (genus Alouatta) and led the state to declare a Public Health Emergency of State Importance, despite no human cases reported. In this study, near-complete genomes of yellow fever virus (YFV) recovered from the outbreak were sequenced and examined aiming at a better understanding of the phylogenetic relationships and the spatio-temporal dynamics of the virus distribution. Our results suggest that the most likely sequence of events involved the reintroduction of YFV from the state of São Paulo to RS through the states of Paraná and Santa Catarina, by the end of 2020. These findings reinforce the role of genomic surveillance in determining the pathways of distribution of the virus and in providing references for the implementation of preventive measures for populations in high risk areas. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

13 pages, 6409 KiB

Open AccessArticle

High Rate of Mutational Events in SARS-CoV-2 Genomes across Brazilian Geographical Regions, February 2020 to June 2021

by Ueric José Borges de Souza, Raíssa Nunes dos Santos, Fabrício Souza Campos, Karine Lima Lourenço, Flavio Guimarães da Fonseca, Fernando Rosado Spilki and Corona-ômica.BR/MCTI Network

Viruses 2021, 13(9), 1806; https://doi.org/10.3390/v13091806 - 10 Sep 2021

Cited by 11 | Viewed by 6219

Abstract

Brazil was considered one of the emerging epicenters of the coronavirus pandemic in 2021, experiencing over 3000 daily deaths caused by the virus at the peak of the second wave. In total, the country had more than 20.8 million confirmed cases of COVID-19, [...] Read more.

Brazil was considered one of the emerging epicenters of the coronavirus pandemic in 2021, experiencing over 3000 daily deaths caused by the virus at the peak of the second wave. In total, the country had more than 20.8 million confirmed cases of COVID-19, including over 582,764 fatalities. A set of emerging variants arose in the country, some of them posing new challenges for COVID-19 control. The goal of this study was to describe mutational events across samples from Brazilian SARS-CoV-2 sequences publicly obtainable on Global Initiative on Sharing Avian Influenza Data-EpiCoV (GISAID-EpiCoV) platform and to generate indexes of new mutations by each genome. A total of 16,953 SARS-CoV-2 genomes were obtained, which were not proportionally representative of the five Brazilian geographical regions. A comparative sequence analysis was conducted to identify common mutations located at 42 positions of the genome (38 were in coding regions, whereas two were in 5′ and two in 3′ UTR). Moreover, 11 were synonymous variants, 27 were missense variants, and more than 44.4% were located in the spike gene. Across the total of single nucleotide variations (SNVs) identified, 32 were found in genomes obtained from all five Brazilian regions. While a high genomic diversity has been reported in Europe given the large number of sequenced genomes, Africa has demonstrated high potential for new variants. In South America, Brazil, and Chile, rates have been similar to those found in South Africa and India, providing enough “space” for new mutations to arise. Genomic surveillance is the central key to identifying the emerging variants of SARS-CoV-2 in Brazil and has shown that the country is one of the “hotspots” in the generation of new variants. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

20 pages, 3671 KiB

Open AccessArticle

The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect

by Safia Zeghbib, Balázs A. Somogyi, Brigitta Zana, Gábor Kemenesi, Róbert Herczeg, Fawzi Derrar and Ferenc Jakab

Viruses 2021, 13(8), 1525; https://doi.org/10.3390/v13081525 - 2 Aug 2021

Cited by 2 | Viewed by 2813

Abstract

To explore the SARS-CoV-2 pandemic in Algeria, a dataset comprising ninety-five genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019, through 4 March 2021, was thoroughly examined. While performing a multi-component analysis regarding the Algerian outbreak, the [...] Read more.

To explore the SARS-CoV-2 pandemic in Algeria, a dataset comprising ninety-five genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019, through 4 March 2021, was thoroughly examined. While performing a multi-component analysis regarding the Algerian outbreak, the toolkit of phylogenetic, phylogeographic, haplotype, and genomic analysis were effectively implemented. We estimated the Time to the Most Recent Common Ancestor (TMRCA) in reference to the Algerian pandemic and highlighted the multiple introductions of the disease and the missing data depicted in the transmission loop. In addition, we emphasized the significant role played by local and international travels in disease dissemination. Most importantly, we unveiled mutational patterns, the effect of unique mutations on corresponding proteins, and the relatedness regarding the Algerian sequences to other sequences worldwide. Our results revealed individual amino-acid replacements such as the deleterious replacement A23T in the orf3a gene in Algeria_EPI_ISL_418241. Additionally, a connection between Algeria_EPI_ISL_420037 and sequences originating from the USA was observed through a USA characteristic amino-acid replacement T1004I in the nsp3 gene, found in the aforementioned Algerian sequence. Similarly, successful tracing could be established, such as Algeria/G37318-8849/2020|EPI_ISL_766863, which was imported from Saudi Arabia during the pilgrimage. Lastly, we assessed the Algerian mitigation measures regarding disease containment using statistical analyses. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

16 pages, 564 KiB

Open AccessArticle

Detection and Genetic Characterization of Hepatitis B and D Viruses: A Multi-Site Cross-Sectional Study of People Who Use Illicit Drugs in the Amazon Region

by Ronylson José S. Silva, Raquel Silva do Nascimento, José Augusto J. Oliveira-Neto, Fabricio Quaresma Silva, Juliana Nádia F. Piauiense, Camila Moraes Gomes, Luiz Marcelo L. Pinheiro, Rafael Lima Resque, João Renato R. Pinho, Emil Kupek, Benedikt Fischer, Luiz Fernando A. Machado, Luísa Caricio Martins, José Alexandre R. Lemos and Aldemir B. Oliveira-Filho

Viruses 2021, 13(7), 1380; https://doi.org/10.3390/v13071380 - 15 Jul 2021

Cited by 4 | Viewed by 2903

Abstract

Hepatitis B (HBV) and delta (HDV) viruses are endemic in the Amazon region, but vaccine coverage against HBV is still limited. People who use illicit drugs (PWUDs) represent a high-risk group due to common risk behavior and socioeconomic factors that facilitate the acquisition [...] Read more.

Hepatitis B (HBV) and delta (HDV) viruses are endemic in the Amazon region, but vaccine coverage against HBV is still limited. People who use illicit drugs (PWUDs) represent a high-risk group due to common risk behavior and socioeconomic factors that facilitate the acquisition and transmission of pathogens. The present study assessed the presence of HBV and HBV-HDV co-infection, identified viral sub-genotypes, and verified the occurrence of mutations in coding regions for HBsAg and part of the polymerase in HBV-infected PWUDs in municipalities of the Brazilian states of Amapá and Pará, in the Amazon region. In total, 1074 PWUDs provided blood samples and personal data in 30 municipalities of the Brazilian Amazon. HBV and HDV were detected by enzyme-linked immunosorbent assay and polymerase chain reaction. Viral genotypes were identified by nucleotide sequencing followed by phylogenetic analysis, whereas viral mutations were analyzed by specialized software. High rates of serological (32.2%) and molecular (7.2%) markers for HBV were detected, including cases of occult HBV infection (2.5%). Sub-genotypes A1, A2, D4, and F2a were most frequently found. Escape mutations due to vaccine and antiviral resistance were identified. Among PWUDs with HBV DNA, serological (19.5%) and molecular (11.7%) HDV markers were detected, such as HDV genotypes 1 and 3. These are worrying findings, presenting clear implications for urgent prevention and treatment needs for the carriers of these viruses. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

16 pages, 2974 KiB

Open AccessArticle

Emergence of a Novel Dengue Virus 3 (DENV-3) Genotype-I Coincident with Increased DENV-3 Cases in Yangon, Myanmar between 2017 and 2019

by Aung Min Soe, Mya Myat Ngwe Tun, Takeshi Nabeshima, Theingi Win Myat, Moh Moh Htun, Htin Lin, Nang Sarm Hom, Shingo Inoue, Khine Mya Nwe, Lynn Pa Pa Aye, Mizuki Fukuta, Kyaw Zin Thant, Futoshi Hasebe, Kouichi Morita, Sujan Shresta, Hlaing Myat Thu and Meng Ling Moi

Viruses 2021, 13(6), 1152; https://doi.org/10.3390/v13061152 - 16 Jun 2021

Cited by 12 | Viewed by 3388

Abstract

Dengue fever, caused by the mosquito-borne dengue virus (DENV), has been endemic in Myanmar since 1970 and it has become a significant public health burden. It is crucial that circulating DENV strains are identified and monitored, and that their transmission efficiency and association [...] Read more.

Dengue fever, caused by the mosquito-borne dengue virus (DENV), has been endemic in Myanmar since 1970 and it has become a significant public health burden. It is crucial that circulating DENV strains are identified and monitored, and that their transmission efficiency and association with disease severity is understood. In this study, we analyzed DENV-1, DENV-2, DENV-3, and DENV-4 serotypes in 1235 serum samples collected in Myanmar between 2017 and 2019. Whole-genome sequencing of DENV-1–4 demonstrated that most DENV-1–4 strains had been circulating in Myanmar for several years. We also identified the emergence of DENV-3 genotype-I in 2017 samples, which persisted through 2018 and 2019. The emergence of the strain coincided with a period of increased DENV-3 cases and marked changes in the serotype dynamics. Nevertheless, we detected no significant differences between serum viral loads, disease severity, and infection status of individuals infected with different DENV serotypes during the 3-year study. Our results not only identify the spread of a new DENV-3 genotype into Yangon, Myanmar, but also support the importance of DENV evolution in changing the epidemic dynamics in endemic regions. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

11 pages, 1775 KiB

Open AccessCommunication

Wa-1 Equine-Like G3P[8] Rotavirus from a Child with Diarrhea in Colombia

by Marlen Martinez-Gutierrez, Estiven Hernandez-Mira, Santiago Rendon-Marin and Julian Ruiz-Saenz

Viruses 2021, 13(6), 1075; https://doi.org/10.3390/v13061075 - 4 Jun 2021

Cited by 4 | Viewed by 2368

Abstract

Rotavirus A (RVA) has been considered the main cause of diarrheal disease in children under five years in emergency services in both developed and developing countries. RVA belongs to the Reoviridae family, which comprises 11 segments of double-stranded RNA (dsRNA) as a genomic [...] Read more.

Rotavirus A (RVA) has been considered the main cause of diarrheal disease in children under five years in emergency services in both developed and developing countries. RVA belongs to the Reoviridae family, which comprises 11 segments of double-stranded RNA (dsRNA) as a genomic constellation that encodes for six structural and five to six nonstructural proteins. RVA has been classified in a binary system with Gx[Px] based on the spike protein (VP4) and the major outer capsid glycoprotein (VP7), respectively. The emerging equine-like G3P[8] DS-1-like strains reported worldwide in humans have arisen an important concern. Here, we carry out the complete genome characterization of a previously reported G3P[8] strain in order to recognize the genetic diversity of RVA circulating among infants in Colombia. A near-full genome phylogenetic analysis was done, confirming the presence of the novel equine-like G3P[8] with a Wa-like backbone for the first time in Colombia. This study demonstrated the importance of surveillance of emerging viruses in the Colombian population; furthermore, additional studies must focus on the understanding of the spread and transmission dynamic of this important RVA strain in different areas of the country. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

14 pages, 10517 KiB

Open AccessArticle

Hepatitis E Virus in People Who Use Crack-Cocaine: A Cross-Sectional Study in a Remote Region of Northern Brazil

by Raquel Silva do Nascimento, Karen Lorena N. Baia, Samara Borges de Souza, Guilherme Martins G. Fontoura, Patrícia Ferreira Nunes, Luiz Fernando A. Machado, Emil Kupek, Benedikt Fischer, Luísa Caricio Martins and Aldemir B. Oliveira-Filho

Viruses 2021, 13(5), 926; https://doi.org/10.3390/v13050926 - 17 May 2021

Cited by 5 | Viewed by 2748

Abstract

People who use crack-cocaine (PWUCC) have numerous vulnerabilities and pose a challenge to health and social assistance services. The exposure to pathogens and risk situations occur differently according to each individual, region and social group. This study identified the presence, genotypes and factors [...] Read more.

People who use crack-cocaine (PWUCC) have numerous vulnerabilities and pose a challenge to health and social assistance services. The exposure to pathogens and risk situations occur differently according to each individual, region and social group. This study identified the presence, genotypes and factors associated with hepatitis E virus (HEV) exposure among a community-recruited cohort of 437 PWUCC in northern Brazil. Epidemiological information was collected through community-based assessments and interviews. Thereafter, blood and fecal samples were collected and tested for HEV using an immunoenzymatic assay, and the genotype was identified by PCR. Logistic regressions were used to identify the risk factors independently associated with exposure to HEV. In total, 79 (18.1%) PWUCC were exposed to HEV: 73 (16.7%) for IgG and six for IgG + IgM. HEV RNA was detected in six fecal samples and in two blood samples from PWUCC with IgM + IgG. Subtype 3c was identified in all of the samples. The factors associated with exposure to HEV were low monthly income, unstable housing (e.g., homelessness), crack-cocaine use ≥40 months, and the shared use of crack-cocaine equipment. The current study provides unique initial insights into HEV status and risk factors among PWUCC in a remote area in Brazil, with diverse implications for urgently improved diagnosis, prevention, and treatment intervention needs. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

8 pages, 1522 KiB

Open AccessCommunication

Limited Genetic Diversity Detected in Middle East Respiratory Syndrome-Related Coronavirus Variants Circulating in Dromedary Camels in Jordan

by Stephanie N. Seifert, Jonathan E. Schulz, Stacy Ricklefs, Michael Letko, Elangeni Yabba, Zaidoun S. Hijazeen, Peter Holloway, Bilal Al-Omari, Hani A. Talafha, Markos Tibbo, Danielle R. Adney, Javier Guitian, Nadim Amarin, Juergen A. Richt, Chester McDowell, John Steel, Ehab A. Abu-Basha, Ahmad M. Al-Majali, Neeltje van Doremalen and Vincent J. Munster

Viruses 2021, 13(4), 592; https://doi.org/10.3390/v13040592 - 31 Mar 2021

Cited by 5 | Viewed by 2822

Abstract

Middle East respiratory syndrome-related coronavirus (MERS-CoV) is a persistent zoonotic pathogen with frequent spillover from dromedary camels to humans in the Arabian Peninsula, resulting in limited outbreaks of MERS with a high case-fatality rate. Full genome sequence data from camel-derived MERS-CoV variants show [...] Read more.

Middle East respiratory syndrome-related coronavirus (MERS-CoV) is a persistent zoonotic pathogen with frequent spillover from dromedary camels to humans in the Arabian Peninsula, resulting in limited outbreaks of MERS with a high case-fatality rate. Full genome sequence data from camel-derived MERS-CoV variants show diverse lineages circulating in domestic camels with frequent recombination. More than 90% of the available full MERS-CoV genome sequences derived from camels are from just two countries, the Kingdom of Saudi Arabia (KSA) and United Arab Emirates (UAE). In this study, we employ a novel method to amplify and sequence the partial MERS-CoV genome with high sensitivity from nasal swabs of infected camels. We recovered more than 99% of the MERS-CoV genome from field-collected samples with greater than 500 TCID₅₀ equivalent per nasal swab from camel herds sampled in Jordan in May 2016. Our subsequent analyses of 14 camel-derived MERS-CoV genomes show a striking lack of genetic diversity circulating in Jordan camels relative to MERS-CoV genome sequences derived from large camel markets in KSA and UAE. The low genetic diversity detected in Jordan camels during our study is consistent with a lack of endemic circulation in these camel herds and reflective of data from MERS outbreaks in humans dominated by nosocomial transmission following a single introduction as reported during the 2015 MERS outbreak in South Korea. Our data suggest transmission of MERS-CoV among two camel herds in Jordan in 2016 following a single introduction event. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

10 pages, 521 KiB

Open AccessArticle

Adjusting the Cut-Off and Maximum Pool Size in RT-qPCR Pool Testing for SARS-CoV-2

by Murilo S. Costa, Hugo I. Sato, Raissa P. Rocha, Alex F. Carvalho, Nathalia S. Guimarães, Elaine L. Machado, Claudia R. L. Alves, Santuza M. R. Teixeira, Ricardo H. C. Takahashi, Unaí Tupinambás and Flávio G. da Fonseca

Viruses 2021, 13(4), 557; https://doi.org/10.3390/v13040557 - 26 Mar 2021

Cited by 5 | Viewed by 2447

Abstract

Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-CoV-2 RNA is an essential test to monitor the occurrence of COVID-19. A methodology is proposed for the determination of maximum pool size and adjustments of cut-off values of cycle threshold ( [...] Read more.

Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-CoV-2 RNA is an essential test to monitor the occurrence of COVID-19. A methodology is proposed for the determination of maximum pool size and adjustments of cut-off values of cycle threshold (

C_{t}

in RT-qPCR pool testing, to compensate for the dilution caused by pooling. The trade-off between pool size and test sensitivity is stated explicitly. The procedure was designed to ensure that samples that would be detectable in individual testing remain detectable in pool testing. The proposed relaxation in cut-off is dependent on the pool size, allowing a relatively tight correction to avoid loss of detection of positive samples. The methodology was evaluated in a study of pool testing of adults attending a public emergency care unit, reference for COVID-19 in Belo Horizonte, Brazil, and presenting flu-like symptoms. Even samples on the edge of detectability in individual testing were detected correctly. The proposed procedure enhances the consistency of RT-qPCR pool testing by enforcing that the scales of detectability in pool processing and in individual sample processing are compatible. This may enhance the contribution of pool testing to large-scale testing for COVID-19. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

17 pages, 1263 KiB

Open AccessArticle

Prevalence and Phylogenetic Analysis of Parvovirus (B19V) among Blood Donors with Different Nationalities Residing in Qatar

by Doua Abdelrahman, Duaa W. Al-Sadeq, Maria K. Smatti, Sara A. Taleb, Raed O AbuOdeh, Enas S. Al-Absi, Asmaa A. Al-Thani, Peter. V. Coyle, Nader Al-Dewik, Ahmed A. Al Qahtani, Hadi M. Yassine and Gheyath K. Nasrallah

Viruses 2021, 13(4), 540; https://doi.org/10.3390/v13040540 - 24 Mar 2021

Cited by 14 | Viewed by 3179

Abstract

Human parvovirus (B19V) is the causative agent of erythema infectiosum in children and is linked to a wide range of clinical manifestations. Studies related to B19V prevalence in the Middle East and North Africa (MENA) region and other parts of Asia are very [...] Read more.

Human parvovirus (B19V) is the causative agent of erythema infectiosum in children and is linked to a wide range of clinical manifestations. Studies related to B19V prevalence in the Middle East and North Africa (MENA) region and other parts of Asia are very scarce. The objectives of this study were to estimate the seroprevalence (anti-B19V IgM and IgG), the viremia rate (B19V DNA), and the circulating genotypes of B19V among blood donors in Qatar. Methods: Donors’ blood samples (n = 5026) from different nationalities, mainly from the MENA region and South East Asia, were collected from 2014–2016. Samples were tested for the B19V DNA using RT-PCR. Furthermore, 1000 selected samples were tested to determine the seroprevalence of B19V antibodies using enzyme-linked immunosorbent assay (ELISA). Genotyping was performed on 65 DNA positive samples by sequencing of nested PCR fragments (NS1-VP1u region, 927 nt). Results: Only 1.4% (70/5026) of the samples had detectible B19V DNA in their blood. B19V DNA prevalence statistically decreased with age (p = 0.03). Anti-B19V IgG was detected in 60.3% (561/930) of the tested samples, while only 2.1% (20/930) were IgM-positive and 1.2% (11/930) were both IgM- and IgG-positive. B19V genotyping showed a predominance of Genotype 1 (100%). Sequence analysis of the NS1-VP1u region revealed 139 mutation sites, some of which were amino acid substitutions. Conclusion: Our results indicated a relatively high seroprevalence of B19V in Qatar. Most importantly, B19 DNA was detected among Qatari and non-Qatari blood donors. Therefore, blood banks in Qatar might need to consider screening for B19V, especially when transfusion is intended for high-risk populations, including immunocompromised patients. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

11 pages, 2320 KiB

Open AccessArticle

Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa

by Susan Engelbrecht, Kayla Delaney, Bronwyn Kleinhans, Eduan Wilkinson, Houriiyah Tegally, Tania Stander, Gert van Zyl, Wolfgang Preiser and Tulio de Oliveira

Viruses 2021, 13(3), 526; https://doi.org/10.3390/v13030526 - 22 Mar 2021

Cited by 18 | Viewed by 5464

Abstract

Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing [...] Read more.

Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 whole genomes. Phylogenetic inference with maximum likelihood and Bayesian methods were used to determine lineages that seeded the local epidemic. Three patients were known to have travelled internationally and an outbreak was detected in a nearby supermarket. Sequencing of 50 samples produced 46 high-quality genomes. The sequences were classified as lineages: B, B.1, B.1.1.1, B.1.1.161, B.1.1.29, B.1.8, B.39, and B.40. All the sequences from persons under investigation (PUIs) in the supermarket outbreak (lineage B.1.8) fall within a clade from the Netherlands with good support (p > 0.9). In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. The molecular clock analysis suggests that this occurred around 13 March 2020 (95% confidence interval: 9–17 March). The phylogenetic reconstruction suggests at least nine early introductions of SARS-CoV-2 into Cape Town and an early localized transmission in a shopping environment. Genomic surveillance was successfully used to investigate and track the spread of early introductions of SARS-CoV-2 in Cape Town. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Graphical abstract

20 pages, 12129 KiB

Open AccessArticle

Human Respiratory Syncytial Virus Infection in a Human T Cell Line Is Hampered at Multiple Steps

by Ricardo de Souza Cardoso, Rosa Maria Mendes Viana, Brenda Cristina Vitti, Ana Carolina Lunardello Coelho, Bruna Laís Santos de Jesus, Juliano de Paula Souza, Marjorie Cornejo Pontelli, Tomoyuki Murakami, Armando Morais Ventura, Akira Ono and Eurico Arruda

Viruses 2021, 13(2), 231; https://doi.org/10.3390/v13020231 - 2 Feb 2021

Cited by 1 | Viewed by 3149

Abstract

Human respiratory syncytial virus (HRSV) is the most frequent cause of severe respiratory disease in children. The main targets of HRSV infection are epithelial cells of the respiratory tract, and the great majority of the studies regarding HRSV infection are done in respiratory [...] Read more.

Human respiratory syncytial virus (HRSV) is the most frequent cause of severe respiratory disease in children. The main targets of HRSV infection are epithelial cells of the respiratory tract, and the great majority of the studies regarding HRSV infection are done in respiratory cells. Recently, the interest on respiratory virus infection of lymphoid cells has been growing, but details of the interaction of HRSV with lymphoid cells remain unknown. Therefore, this study was done to assess the relationship of HRSV with A3.01 cells, a human CD4⁺ T cell line. Using flow cytometry and fluorescent focus assay, we found that A3.01 cells are susceptible but virtually not permissive to HRSV infection. Dequenching experiments revealed that the fusion process of HRSV in A3.01 cells was nearly abolished in comparison to HEp-2 cells, an epithelial cell lineage. Quantification of viral RNA by RT-qPCR showed that the replication of HRSV in A3.01 cells was considerably reduced. Western blot and quantitative flow cytometry analyses demonstrated that the production of HRSV proteins in A3.01 was significantly lower than in HEp-2 cells. Additionally, using fluorescence in situ hybridization, we found that the inclusion body-associated granules (IBAGs) were almost absent in HRSV inclusion bodies in A3.01 cells. We also assessed the intracellular trafficking of HRSV proteins and found that HRSV proteins colocalized partially with the secretory pathway in A3.01 cells, but these HRSV proteins and viral filaments were present only scarcely at the plasma membrane. HRSV infection of A3.01 CD4⁺ T cells is virtually unproductive as compared to HEp-2 cells, as a result of defects at several steps of the viral cycle: Fusion, genome replication, formation of inclusion bodies, recruitment of cellular proteins, virus assembly, and budding. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Graphical abstract

18 pages, 4018 KiB

Open AccessArticle

Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil

by Marcelo Henrique Santos Paiva, Duschinka Ribeiro Duarte Guedes, Cássia Docena, Matheus Filgueira Bezerra, Filipe Zimmer Dezordi, Laís Ceschini Machado, Larissa Krokovsky, Elisama Helvecio, Alexandre Freitas da Silva, Luydson Richardson Silva Vasconcelos, Antonio Mauro Rezende, Severino Jefferson Ribeiro da Silva, Kamila Gaudêncio da Silva Sales, Bruna Santos Lima Figueiredo de Sá, Derciliano Lopes da Cruz, Claudio Eduardo Cavalcanti, Armando de Menezes Neto, Caroline Targino Alves da Silva, Renata Pessôa Germano Mendes, Maria Almerice Lopes da Silva, Tiago Gräf, Paola Cristina Resende, Gonzalo Bello, Michelle da Silva Barros, Wheverton Ricardo Correia do Nascimento, Rodrigo Moraes Loyo Arcoverde, Luciane Caroline Albuquerque Bezerra, Sinval Pinto Brandão-Filho, Constância Flávia Junqueira Ayres and Gabriel Luz Wallau Show full author list Hide full author list

Viruses 2020, 12(12), 1414; https://doi.org/10.3390/v12121414 - 9 Dec 2020

Cited by 36 | Viewed by 6733

Abstract

Multiple epicenters of the SARS-CoV-2 pandemic have emerged since the first pneumonia cases in Wuhan, China, such as Italy, USA, and Brazil. Brazil is the third-most affected country worldwide, but genomic sequences of SARS-CoV-2 strains are mostly restricted to states from the Southeast [...] Read more.

Multiple epicenters of the SARS-CoV-2 pandemic have emerged since the first pneumonia cases in Wuhan, China, such as Italy, USA, and Brazil. Brazil is the third-most affected country worldwide, but genomic sequences of SARS-CoV-2 strains are mostly restricted to states from the Southeast region. Pernambuco state, located in the Northeast region, is the sixth most affected Brazilian state, but very few genomic sequences from the strains circulating in this region are available. We sequenced 101 strains of SARS-CoV-2 from patients presenting Covid-19 symptoms that reside in Pernambuco. Phylogenetic reconstructions revealed that all genomes belong to the B lineage and most of the samples (88%) were classified as lineage B.1.1. We detected multiple viral introductions from abroad (likely from Europe) as well as six local B.1.1 clades composed by Pernambuco only strains. Local clades comprise sequences from the capital city (Recife) and other country-side cities, corroborating the community spread between different municipalities of the state. These findings demonstrate that different from Southeastern Brazilian states where the epidemics were majorly driven by one dominant lineage (B.1.1.28 or B.1.1.33), the early epidemic phase at the Pernambuco state was driven by multiple B.1.1 lineages seeded through both national and international traveling. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

Review

Jump to: Editorial, Research, Other

15 pages, 788 KiB

Open AccessReview

Towards Integrated Management of Dengue in Mumbai

by Prasad N. Paradkar, Pallavi R. Sahasrabudhe, Mrunal Ghag Sawant, Sandeepan Mukherjee and Kim R. Blasdell

Viruses 2021, 13(12), 2436; https://doi.org/10.3390/v13122436 - 4 Dec 2021

Cited by 5 | Viewed by 3892

Abstract

With increasing urbanisation, the dengue disease burden is on the rise in India, especially in large cities such as Mumbai. Current dengue surveillance in Mumbai includes municipal corporation carrying out specific activities to reduce mosquito breeding sites and the use of insecticides to [...] Read more.

With increasing urbanisation, the dengue disease burden is on the rise in India, especially in large cities such as Mumbai. Current dengue surveillance in Mumbai includes municipal corporation carrying out specific activities to reduce mosquito breeding sites and the use of insecticides to suppress the adult mosquito populations. Clinical cases remain either underreported or misreported due to the restriction to government clinics, missing the large private health care sector. There is a need for an integrated approach to manage dengue outbreaks in Mumbai. There are various novel strategies available for use that can be utilised to improve disease detection, mosquito surveillance, and control of mosquito-borne diseases. These novel technologies are discussed in this manuscript. Given the complex ecosystem of mosquito-borne diseases in Mumbai, integrating data obtained from these technologies would support the ongoing mosquito control measures in Mumbai. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

32 pages, 3309 KiB

Open AccessReview

Viral and Prion Infections Associated with Central Nervous System Syndromes in Brazil

by Ivanildo P. Sousa, Jr., Flavia B. dos Santos, Vanessa S. de Paula, Tuane C.R.G. Vieira, Helver G. Dias, Caroline A. Barros and Edson E. da Silva

Viruses 2021, 13(7), 1370; https://doi.org/10.3390/v13071370 - 15 Jul 2021

Cited by 10 | Viewed by 5369

Abstract

Virus-induced infections of the central nervous system (CNS) are among the most serious problems in public health and can be associated with high rates of morbidity and mortality, mainly in low- and middle-income countries, where these manifestations have been neglected. Typically, herpes simplex [...] Read more.

Virus-induced infections of the central nervous system (CNS) are among the most serious problems in public health and can be associated with high rates of morbidity and mortality, mainly in low- and middle-income countries, where these manifestations have been neglected. Typically, herpes simplex virus 1 and 2, varicella-zoster, and enterovirus are responsible for a high number of cases in immunocompetent hosts, whereas other herpesviruses (for example, cytomegalovirus) are the most common in immunocompromised individuals. Arboviruses have also been associated with outbreaks with a high burden of neurological disorders, such as the Zika virus epidemic in Brazil. There is a current lack of understanding in Brazil about the most common viruses involved in CNS infections. In this review, we briefly summarize the most recent studies and findings associated with the CNS, in addition to epidemiological data that provide extensive information on the circulation and diversity of the most common neuro-invasive viruses in Brazil. We also highlight important aspects of the prion-associated diseases. This review provides readers with better knowledge of virus-associated CNS infections. A deeper understanding of these infections will support the improvement of the current surveillance strategies to allow the timely monitoring of the emergence/re-emergence of neurotropic viruses. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

25 pages, 798 KiB

Open AccessReview

The Epidemiological Impact of STIs among General and Vulnerable Populations of the Amazon Region of Brazil: 30 years of Surveillance

by Luiz Fernando Almeida Machado, Ricardo Roberto de Souza Fonseca, Maria Alice Freitas Queiroz, Aldemir Branco Oliveira-Filho, Izaura Maria Vieira Cayres-Vallinoto, Antonio Carlos Rosário Vallinoto, Marluísa de Oliveira Guimarães Ishak and Ricardo Ishak

Viruses 2021, 13(5), 855; https://doi.org/10.3390/v13050855 - 7 May 2021

Cited by 10 | Viewed by 3368

Abstract

Sexually transmitted infections (STIs) represent a worldwide public health problem and, although many of them are curable, they continue to be neglected, especially in areas with a low human development index, such as in the northern region of Brazil. This review describes the [...] Read more.

Sexually transmitted infections (STIs) represent a worldwide public health problem and, although many of them are curable, they continue to be neglected, especially in areas with a low human development index, such as in the northern region of Brazil. This review describes the results of 30 years of studies at the Virus Laboratory at the Federal University of Pará, including the prevalence and molecular epidemiology of HIV-1, HTLV-1/2, HPV, HBV, Treponema pallidum and Chlamydia trachomatis among urban and non-urban populations, and also in vulnerable groups in the Brazilian Amazon. Control strategies and challenges in preventing STIs are discussed considering this immense geographic region, where essential health services are unable to reach the entire population, especially the most vulnerable, such as female sex workers, people who use illicit drugs, remnants of quilombolos and indigenous communities. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

17 pages, 3398 KiB

Open AccessReview

Dengue Virus Infection and Associated Risk Factors in Africa: A Systematic Review and Meta-Analysis

by Gaspary O. Mwanyika, Leonard E. G. Mboera, Sima Rugarabamu, Baraka Ngingo, Calvin Sindato, Julius J. Lutwama, Janusz T. Paweska and Gerald Misinzo

Viruses 2021, 13(4), 536; https://doi.org/10.3390/v13040536 - 24 Mar 2021

Cited by 27 | Viewed by 6312

Abstract

Dengue contributes a significant burden on global public health and economies. In Africa, the burden of dengue virus (DENV) infection is not well described. This review was undertaken to determine the prevalence of dengue and associated risk factors. A literature search was done [...] Read more.

Dengue contributes a significant burden on global public health and economies. In Africa, the burden of dengue virus (DENV) infection is not well described. This review was undertaken to determine the prevalence of dengue and associated risk factors. A literature search was done on PubMed/MEDLINE, Scopus, Embase, and Google Scholar databases to identify articles published between 1960 and 2020. Meta-analysis was performed using a random-effect model at a 95% confidence interval, followed by subgroup meta-analysis to determine the overall prevalence. Between 1960 and 2020, 45 outbreaks were identified, of which 17 and 16 occurred in East and West Africa, respectively. Dengue virus serotype 1 (DENV-1) and DENV-2 were the dominant serotypes contributing to 60% of the epidemics. Of 2211 cases reported between 2009 and 2020; 1954 (88.4%) were reported during outbreaks. Overall, the prevalence of dengue was 29% (95% CI: 20–39%) and 3% (95% CI: 1–5%) during the outbreak and non-outbreak periods, respectively. Old age (6/21 studies), lack of mosquito control (6/21), urban residence (4/21), climate change (3/21), and recent history of travel (3/21) were the leading risk factors. This review reports a high burden of dengue and increased risk of severe disease in Africa. Our findings provide useful information for clinical practice and health policy decisions to implement effective interventions. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

29 pages, 1250 KiB

Open AccessReview

In Vitro and In Vivo Models for Studying SARS-CoV-2, the Etiological Agent Responsible for COVID-19 Pandemic

by Rafael B. Rosa, Willyenne M. Dantas, Jessica C. F. do Nascimento, Murilo V. da Silva, Ronaldo N. de Oliveira and Lindomar J. Pena

Viruses 2021, 13(3), 379; https://doi.org/10.3390/v13030379 - 27 Feb 2021

Cited by 57 | Viewed by 8196

Abstract

The emergence and rapid worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has prompted the scientific community to rapidly develop in vitro and in vivo models that could be applied in COVID-19 research. In vitro models include two-dimensional (2D) cultures of [...] Read more.

The emergence and rapid worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has prompted the scientific community to rapidly develop in vitro and in vivo models that could be applied in COVID-19 research. In vitro models include two-dimensional (2D) cultures of immortalized cell lines or primary cells and three-dimensional (3D) cultures derived from lung, alveoli, bronchi, and other organs. Although cell-based systems are economic and allow strict control of experimental variables, they do not always resemble physiological conditions. Thus, several in vivo models are being developed, including different strains of mice, hamsters, ferrets, dogs, cats, and non-human primates. In this review, we summarize the main models of SARS-CoV-2 infection developed so far and discuss their advantages, drawbacks and main uses. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

Other

Jump to: Editorial, Research, Review

12 pages, 1872 KiB

Open AccessBrief Report

Yellow Fever Outbreak in Eastern Senegal, 2020–2021

by Moussa Moïse Diagne, Marie Henriette Dior Ndione, Alioune Gaye, Mamadou Aliou Barry, Diawo Diallo, Amadou Diallo, Lusajo L. Mwakibete, Mamadou Diop, El Hadji Ndiaye, Vida Ahyong, Babacar Diouf, Moufid Mhamadi, Cheikh Tidiane Diagne, Fodé Danfakha, Boly Diop, Oumar Faye, Cheikh Loucoubar, Gamou Fall, Cristina M. Tato, Amadou Alpha Sall, Scott C. Weaver, Mawlouth Diallo and Ousmane Faye Show full author list Hide full author list

Viruses 2021, 13(8), 1475; https://doi.org/10.3390/v13081475 - 28 Jul 2021

Cited by 15 | Viewed by 3871

Abstract

Yellow fever virus remains a major threat in low resource countries in South America and Africa despite the existence of an effective vaccine. In Senegal and particularly in the eastern part of the country, periodic sylvatic circulation has been demonstrated with varying degrees [...] Read more.

Yellow fever virus remains a major threat in low resource countries in South America and Africa despite the existence of an effective vaccine. In Senegal and particularly in the eastern part of the country, periodic sylvatic circulation has been demonstrated with varying degrees of impact on populations in perpetual renewal. We report an outbreak that occurred from October 2020 to February 2021 in eastern Senegal, notified and managed through the synergistic effort yellow fever national surveillance implemented by the Senegalese Ministry of Health in collaboration with the World Health Organization, the countrywide 4S network set up by the Ministry of Health, the Institut Pasteur de Dakar, and the surveillance of arboviruses and hemorrhagic fever viruses in human and vector populations implemented since mid 2020 in eastern Senegal. Virological analyses highlighted the implication of sylvatic mosquito species in virus transmission. Genomic analysis showed a close relationship between the circulating strain in eastern Senegal, 2020, and another one from the West African lineage previously detected and sequenced two years ago from an unvaccinated Dutch traveler who visited the Gambia and Senegal before developing signs after returning to Europe. Moreover, genome analysis identified a 6-nucleotide deletion in the variable domain of the 3′UTR with potential impact on the biology of the viral strain that merits further investigations. Integrated surveillance of yellow fever virus but also of other arboviruses of public health interest is crucial in an ecosystem such as eastern Senegal. Full article

(This article belongs to the Special Issue Viral Infections in Developing Countries)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Viral Infections in Developing Countries

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Related Special Issue

Published Papers (26 papers)

Editorial

Research

Review

Other

Further Information

Guidelines

MDPI Initiatives

Follow MDPI