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Viruses
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SARS-CoV-2 Genomics
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SARS-CoV-2 Genomics

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "SARS-CoV-2 and COVID-19".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 38454

Special Issue Editors

Dr. Judd F. Hultquist

E-Mail Website
Guest Editor
Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
Interests: virology; systems biology; host-pathogen interactions
Dr. Ramón Lorenzo-Redondo

E-Mail Website
Guest Editor
Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
Interests: viral evolution; population dynamics; phylogenetics
Dr. Egon Anderson Ozer

E-Mail Website
Guest Editor
Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
Interests: antimicrobial resistance; pathogen genomics

Special Issue Information

Dear Colleagues,

The ongoing evolution of severe acute respiratory syndrome coronavirus (SARS-CoV-2) has complicated efforts to combat the global COVID-19 pandemic. The emergence of new variants of concern with enhanced transmissibility, decreased susceptibility to neutralizing antibodies, and/or decreased susceptibility to therapeutic agents has highlighted the urgent need for continued genomic surveillance across the globe. Many obstacles remain to be overcome in the collection, interpretation, dissemination, and application of these data to medicine and public health. Challenges include sampling inequities, inadequate linkage to clinical metadata, lack of expertise/resources, and delayed reporting/dissemination, among others.

The aim of the Special Issue is to provide data on the causes and consequences of the ongoing evolution of SARS-CoV-2, including descriptions of technical innovations underlying new discoveries, analyses of the functional and clinical relevance of novel variants, explorations of the molecular epidemiology of the virus in different regions around the globe as the pandemic enters its third year, and perspectives towards improving translational research in infectious disease. We anticipate the reports collected in this issue will be of considerable interest and value to the scientific, clinical, and public health communities as they manage this pandemic and prepare for the next.

Dr. Judd F. Hultquist
Dr. Ramón Lorenzo-Redondo
Dr. Egon Anderson Ozer
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • SARS-CoV-2
  • COVID-19
  • Variants of concern
  • Molecular epidemiology
  • Mutation
  • Evolution
  • Phylogenetics
  • Public Health
  • Global Health
  • Translational Research

Published Papers (16 papers)

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Research

Jump to: Review, Other

18 pages, 2667 KiB  
Article
ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes
by Arghavan Alisoltani, Lukasz Jaroszewski, Adam Godzik, Arash Iranzadeh, Lacy M. Simons, Taylor J. Dean, Ramon Lorenzo-Redondo, Judd F. Hultquist and Egon A. Ozer
Viruses 2022, 14(12), 2714; https://doi.org/10.3390/v14122714 - 05 Dec 2022
Cited by 3 | Viewed by 1980
Abstract
The unprecedented growth of publicly available SARS-CoV-2 genome sequence data has increased the demand for effective and accessible SARS-CoV-2 data analysis and visualization tools. The majority of the currently available tools either require computational expertise to deploy them or limit user input to [...] Read more.
The unprecedented growth of publicly available SARS-CoV-2 genome sequence data has increased the demand for effective and accessible SARS-CoV-2 data analysis and visualization tools. The majority of the currently available tools either require computational expertise to deploy them or limit user input to preselected subsets of SARS-CoV-2 genomes. To address these limitations, we developed ViralVar, a publicly available, point-and-click webtool that gives users the freedom to investigate and visualize user-selected subsets of SARS-CoV-2 genomes obtained from the GISAID public database. ViralVar has two primary features that enable: (1) the visualization of the spatiotemporal dynamics of SARS-CoV-2 lineages and (2) a structural/functional analysis of genomic mutations. As proof-of-principle, ViralVar was used to explore the evolution of the SARS-CoV-2 pandemic in the USA in pediatric, adult, and elderly populations (n > 1.7 million genomes). Whereas the spatiotemporal dynamics of the variants did not differ between these age groups, several USA-specific sublineages arose relative to the rest of the world. Our development and utilization of ViralVar to provide insights on the evolution of SARS-CoV-2 in the USA demonstrates the importance of developing accessible tools to facilitate and accelerate the large-scale surveillance of circulating pathogens. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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10 pages, 1181 KiB  
Article
SARS-CoV-2 Variants Identification; A Fast and Affordable Strategy Based on Partial S-Gene Targeted PCR Sequencing
by Antonio Martínez-Murcia, Adrian Garcia-Sirera, Aaron Navarro and Laura Pérez
Viruses 2022, 14(11), 2588; https://doi.org/10.3390/v14112588 - 21 Nov 2022
Cited by 2 | Viewed by 1422 | Correction
Abstract
A considerable number of new SARS-CoV-2 lineages have emerged since the first COVID-19 cases were reported in Wuhan. As a few variants showed higher COVID-19 disease transmissibility and the ability to escape from immune responses, surveillance became relevant at that time. Single-nucleotide mutation [...] Read more.
A considerable number of new SARS-CoV-2 lineages have emerged since the first COVID-19 cases were reported in Wuhan. As a few variants showed higher COVID-19 disease transmissibility and the ability to escape from immune responses, surveillance became relevant at that time. Single-nucleotide mutation PCR-based protocols were not always specific, and consequently, determination of a high number of informative sites was needed for accurate lineage identification. A detailed in silico analysis of SARS-CoV-2 sequences retrieved from GISAID database revealed the S gene 921 bp-fragment, positions 22784–23705 of SARS-CoV-2 reference genome, as the most informative fragment (30 variable sites) to determine relevant SARS-CoV-2 variants. Consequently, a method consisting of the PCR-amplification of this fragment, followed by Sanger’s sequencing and a “single-click” informatic program based on a reference database, was developed and validated. PCR-fragments obtained from clinical SARS-CoV-2 samples were compared with homologous variant-sequences and the resulting phylogenetic tree allowed the identification of Alpha, Delta, Omicron, Beta, Gamma, and other variants. The data analysis procedure was automatized and simplified to the point that it did not require specific technical skills. The method is faster and cheaper than current whole-genome sequencing methods; it is available worldwide, and it may help to enhance efficient surveillance in the fight against the COVID-19 pandemic. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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25 pages, 8498 KiB  
Article
Predicting Epitope Candidates for SARS-CoV-2
by Akshay Agarwal, Kristen L. Beck, Sara Capponi, Mark Kunitomi, Gowri Nayar, Edward Seabolt, Gandhar Mahadeshwar, Simone Bianco, Vandana Mukherjee and James H. Kaufman
Viruses 2022, 14(8), 1837; https://doi.org/10.3390/v14081837 - 21 Aug 2022
Cited by 3 | Viewed by 2237
Abstract
Epitopes are short amino acid sequences that define the antigen signature to which an antibody or T cell receptor binds. In light of the current pandemic, epitope analysis and prediction are paramount to improving serological testing and developing vaccines. In this paper, known [...] Read more.
Epitopes are short amino acid sequences that define the antigen signature to which an antibody or T cell receptor binds. In light of the current pandemic, epitope analysis and prediction are paramount to improving serological testing and developing vaccines. In this paper, known epitope sequences from SARS-CoV, SARS-CoV-2, and other Coronaviridae were leveraged to identify additional antigen regions in 62K SARS-CoV-2 genomes. Additionally, we present epitope distribution across SARS-CoV-2 genomes, locate the most commonly found epitopes, and discuss where epitopes are located on proteins and how epitopes can be grouped into classes. The mutation density of different protein regions is presented using a big data approach. It was observed that there are 112 B cell and 279 T cell conserved epitopes between SARS-CoV-2 and SARS-CoV, with more diverse sequences found in Nucleoprotein and Spike glycoprotein. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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17 pages, 1922 KiB  
Article
Sequencing during Times of Change: Evaluating SARS-CoV-2 Clinical Samples during the Transition from the Delta to Omicron Wave
by Shuchen Feng, Mudassir S. Ali, Monika Evdokimova, Gail E. Reid, Nina M. Clark, Susan L. Uprichard and Susan C. Baker
Viruses 2022, 14(7), 1408; https://doi.org/10.3390/v14071408 - 28 Jun 2022
Cited by 3 | Viewed by 1731
Abstract
The pandemic of SARS-CoV-2 is characterized by the emergence of new variants of concern (VOCs) that supplant previous waves of infection. Here, we describe our investigation of the lineages and host-specific mutations identified in a particularly vulnerable population of predominantly older and immunosuppressed [...] Read more.
The pandemic of SARS-CoV-2 is characterized by the emergence of new variants of concern (VOCs) that supplant previous waves of infection. Here, we describe our investigation of the lineages and host-specific mutations identified in a particularly vulnerable population of predominantly older and immunosuppressed SARS-CoV-2-infected patients seen at our medical center in Chicago during the transition from the Delta to Omicron wave. We compare two primer schemes, ArticV4.1 and VarSkip2, used for short read amplicon sequencing, and describe our strategy for bioinformatics analysis that facilitates identifying lineage-associated mutations and host-specific mutations that arise during infection. This study illustrates the ongoing evolution of SARS-CoV-2 VOCs in our community and documents novel constellations of mutations that arise in individual patients. The ongoing evaluation of the evolution of SARS-CoV-2 during this pandemic is important for informing our public health strategies. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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9 pages, 3092 KiB  
Article
SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay
by Steven C. Holland, Ajeet Bains, LaRinda A. Holland, Matthew F. Smith, Regan A. Sullins, Nicholas J. Mellor, Alexis W. Thomas, Nathaniel Johnson, Vel Murugan and Efrem S. Lim
Viruses 2022, 14(6), 1316; https://doi.org/10.3390/v14061316 - 16 Jun 2022
Cited by 8 | Viewed by 2237
Abstract
As the SARS-CoV-2 virus evolves, mutations may result in diminished sensitivity to qRT-PCR diagnostic assays. We investigated four polymorphisms circulating in the SARS-CoV-2 Delta lineage that result in N gene target failure (NGTF) on the TaqPath COVID-19 Combo Kit. These mutations were detected [...] Read more.
As the SARS-CoV-2 virus evolves, mutations may result in diminished sensitivity to qRT-PCR diagnostic assays. We investigated four polymorphisms circulating in the SARS-CoV-2 Delta lineage that result in N gene target failure (NGTF) on the TaqPath COVID-19 Combo Kit. These mutations were detected from the SARS-CoV-2 genome sequences that matched with the diagnostic assay results of saliva specimens. Full length N genes from the samples displaying NGTF were cloned into plasmids and assayed using three SARS-CoV-2 qRT-PCR assays. These constructs resulted in reduced sensitivity to the TaqPath COVID-19 Combo Kit compared to the controls (mean Ct differences of 3.06, 7.70, 12.46, and 14.12), but were detected equivalently on the TaqPath COVID-19 Fast PCR Combo 2.0 or CDC 2019_nCoV_N2 assays. This work highlights the importance of genomic sequencing to monitor circulating mutations and provide guidance in improving diagnostic assays. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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12 pages, 3668 KiB  
Article
Sequential Appearance and Isolation of a SARS-CoV-2 Recombinant between Two Major SARS-CoV-2 Variants in a Chronically Infected Immunocompromised Patient
by Emilie Burel, Philippe Colson, Jean-Christophe Lagier, Anthony Levasseur, Marielle Bedotto, Philippe Lavrard-Meyer, Pierre-Edouard Fournier, Bernard La Scola and Didier Raoult
Viruses 2022, 14(6), 1266; https://doi.org/10.3390/v14061266 - 10 Jun 2022
Cited by 15 | Viewed by 3074
Abstract
Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but only a [...] Read more.
Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but only a single patient’s sample was analyzed, and the virus was not isolated. Here, we report the gradual emergence of a hybrid genome of B.1.160 and Alpha variants in a lymphoma patient chronically infected for 14 months, and we isolated the recombinant virus. The hybrid genome was obtained by next-generation sequencing, and the recombination sites were confirmed by PCR. This consisted of a parental B.1.160 backbone interspersed with two fragments, including the spike gene, from an Alpha variant. An analysis of seven sequential samples from the patient decoded the recombination steps, including the initial infection with a B.1.160 variant, then a concurrent infection with this variant and an Alpha variant, the generation of hybrid genomes, and eventually the emergence of a predominant recombinant virus isolated at the end of the patient’s follow-up. This case exemplifies the recombination process of SARS-CoV-2 in real life, and it calls for intensifying the genomic surveillance in patients coinfected with different SARS-CoV-2 variants, and more generally with several RNA viruses, as this may lead to the appearance of new viruses. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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11 pages, 2797 KiB  
Article
Detecting Potentially Adaptive Mutations from the Parallel and Fixed Patterns in SARS-CoV-2 Evolution
by Cheng-Yang Ji, Na Han, Ye-Xiao Cheng, Jingzhe Shang, Shenghui Weng, Rong Yang, Hang-Yu Zhou and Aiping Wu
Viruses 2022, 14(5), 1087; https://doi.org/10.3390/v14051087 - 18 May 2022
Cited by 4 | Viewed by 2082
Abstract
Early identification of adaptive mutations could provide timely help for the control and prevention of the COVID-19 pandemic. The fast accumulation of SARS-CoV-2 sequencing data provides important support, while also raising a great challenge for the recognition of adaptive mutations. Here, we proposed [...] Read more.
Early identification of adaptive mutations could provide timely help for the control and prevention of the COVID-19 pandemic. The fast accumulation of SARS-CoV-2 sequencing data provides important support, while also raising a great challenge for the recognition of adaptive mutations. Here, we proposed a computational strategy to detect potentially adaptive mutations from their fixed and parallel patterns in the phylogenetic trajectory. We found that the biological meanings of fixed substitution and parallel mutation are highly complementary, and can reasonably be integrated as a fixed and parallel (paraFix) mutation, to identify potentially adaptive mutations. Tracking the dynamic evolution of SARS-CoV-2, 37 sites in spike protein were identified as having experienced paraFix mutations. Interestingly, 70% (26/37) of them have already been experimentally confirmed as adaptive mutations. Moreover, most of the mutations could be inferred as paraFix mutations one month earlier than when they became regionally dominant. Overall, we believe that the concept of paraFix mutations will help researchers to identify potentially adaptive mutations quickly and accurately, which will provide invaluable clues for disease control and prevention. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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14 pages, 1698 KiB  
Article
Molecular Analysis of SARS-CoV-2 Lineages in Armenia
by Diana Avetyan, Siras Hakobyan, Maria Nikoghosyan, Lilit Ghukasyan, Gisane Khachatryan, Tamara Sirunyan, Nelli Muradyan, Roksana Zakharyan, Andranik Chavushyan, Varduhi Hayrapetyan, Anahit Hovhannisyan, Shah A. Mohamed Bakhash, Keith R. Jerome, Pavitra Roychoudhury, Alexander L. Greninger, Lyudmila Niazyan, Mher Davidyants, Gayane Melik-Andreasyan, Shushan Sargsyan, Lilit Nersisyan and Arsen Arakelyanadd Show full author list remove Hide full author list
Viruses 2022, 14(5), 1074; https://doi.org/10.3390/v14051074 - 17 May 2022
Cited by 6 | Viewed by 3024
Abstract
The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina sequencing to describe the circulation of the virus lineages in Armenia. The analysis of 145 full [...] Read more.
The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina sequencing to describe the circulation of the virus lineages in Armenia. The analysis of 145 full genomes identified six clades (19A, 20A, 20B, 20I, 21J, and 21K) and considerable intra-clade PANGO lineage diversity. Phylodynamic and transmission analysis allowed to attribute specific clades as well as infer their importation routes. Thus, the first two waves of positive case increase were caused by the 20B clade, the third peak caused by the 20I (Alpha), while the last two peaks were caused by the 21J (Delta) and 21K (Omicron) variants. The functional analyses of mutations in sequences largely affected epitopes associated with protective HLA loci and did not cause the loss of the signal in PCR tests targeting ORF1ab and N genes as confirmed by RT-PCR. We also compared the performance of nanopore and Illumina short-read sequencing and showed the utility of nanopore sequencing as an efficient and affordable alternative for large-scale molecular epidemiology research. Thus, our paper describes new data on the genomic diversity of SARS-CoV-2 variants in Armenia in the global context of the virus molecular genomic surveillance. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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16 pages, 4477 KiB  
Article
SARS-CoV-2 Lineage A.27: New Data from African Countries and Dynamics in the Context of the COVID-19 Pandemic
by Anissa Chouikha, Adamou Lagare, Kais Ghedira, Amadou Diallo, Richard Njouom, Safietou Sankhe, Fawzi Derrar, Kathleen Victoir, Koussay Dellagi, Henda Triki and Moussa Moise Diagne
Viruses 2022, 14(5), 1007; https://doi.org/10.3390/v14051007 - 09 May 2022
Cited by 4 | Viewed by 1990
Abstract
SARS-CoV-2 is constantly evolving with lineages emerging and others eclipsing. Some lineages have an important epidemiological impact and are known as variants of interest (VOIs), variants under monitoring (VUMs) or variants of concern (VOCs). Lineage A.27 was first defined as a VUM since [...] Read more.
SARS-CoV-2 is constantly evolving with lineages emerging and others eclipsing. Some lineages have an important epidemiological impact and are known as variants of interest (VOIs), variants under monitoring (VUMs) or variants of concern (VOCs). Lineage A.27 was first defined as a VUM since it holds mutations of concern. Here, we report additional lineage A.27 data and sequences from five African countries and describe the molecular characteristics, and the genetic history of this lineage worldwide. Based on the new sequences investigated, the most recent ancestor (tMRCA) of lineage A.27 was estimated to be from April 2020 from Niger. It then spread to Europe and other parts of the world with a peak observed between February and April 2021. The detection rate of A.27 then decreased with only a few cases reported during summer 2021. The phylogenetic analysis revealed many sub-lineages. Among them, one was defined by the substitution Q677H in the spike (S) gene, one was defined by the substitution D358N in the nucleoprotein (N) gene and one was defined by the substitution A2143V in the ORF1b gene. This work highlights the importance of molecular characterization and the timely submission of sequences to correctly describe the circulation of particular strains in order to be proactive in monitoring the pandemic. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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14 pages, 1751 KiB  
Article
Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19
by Anissa Chouikha, Wasfi Fares, Asma Laamari, Sondes Haddad-Boubaker, Zeineb Belaiba, Kais Ghedira, Wafa Kammoun Rebai, Kaouther Ayouni, Marwa Khedhiri, Samar Ben Halima, Henda Krichen, Henda Touzi, Imen Ben Dhifallah, Fatma Z. Guerfali, Chiraz Atri, Saifeddine Azouz, Oussema Khamessi, Monia Ardhaoui, Mouna Safer, Nissaf Ben Alaya, Ikram Guizani, Rym Kefi, Mariem Gdoura and Henda Trikiadd Show full author list remove Hide full author list
Viruses 2022, 14(3), 624; https://doi.org/10.3390/v14030624 - 17 Mar 2022
Cited by 11 | Viewed by 3145
Abstract
Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and [...] Read more.
Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and deaths. The present study provides genetic information on the different lineages of SARS-CoV-2 that circulated in Tunisia over 17 months. Lineages were assigned for 1359 samples using whole-genome sequencing, partial S gene sequencing and variant-specific real-time RT-PCR tests. Forty-eight different lineages of SARS-CoV-2 were identified, including variants of concern (VOCs), variants of interest (VOIs) and variants under monitoring (VUMs), particularly Alpha, Beta, Delta, A.27, Zeta and Eta. The first wave, limited to imported and import-related cases, was characterized by a small number of positive samples and lineages. During the second wave, a large number of lineages were detected; the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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17 pages, 3704 KiB  
Article
Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City
by Alberto Cedro-Tanda, Laura Gómez-Romero, Guillermo de Anda-Jauregui, Dora Garnica-López, Yair Alfaro-Mora, Sonia Sánchez-Xochipa, Eulices F. García-García, Alfredo Mendoza-Vargas, Emmanuel J. Frías-Jiménez, Bernardo Moreno, Abraham Campos-Romero, José L. Moreno-Camacho, Jonathan Alcantar-Fernández, Jesús Ortíz-Ramírez, Mariana Benitez-González, Roxana Trejo-González, Daniel Aguirre-Chavarría, Marcela E. Núñez-Martínez, Laura Uribe-Figueroa, Ofelia Angulo, Rosaura Ruiz, Alfredo Hidalgo-Miranda and Luis A. Herreraadd Show full author list remove Hide full author list
Viruses 2022, 14(3), 545; https://doi.org/10.3390/v14030545 - 06 Mar 2022
Cited by 20 | Viewed by 3693
Abstract
Omicron is the most mutated SARS-CoV-2 variant—a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results. From 16 November to 31 December [...] Read more.
Omicron is the most mutated SARS-CoV-2 variant—a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results. From 16 November to 31 December 2021, we observed an increase of 88% in Omicron prevalence in Mexico City. We explored the R346K substitution, prevalent in 42% of Omicron variants, known to be associated with immune escape by monoclonal antibodies. In a phylogenetic analysis, we found several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. A haplotype analysis revealed that there was no association between haplotype and vaccination status. Among the 66% of patients who have been vaccinated, no reported comorbidities were associated with Omicron; the presence of odynophagia and the absence of dysgeusia were significant predictor symptoms for Omicron, and the RT-qPCR Ct values were lower for Omicron. Conclusions. Genomic surveillance is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, and can inform public health decisions and detect the spread of any mutation that may affect therapeutic efficacy. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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7 pages, 409 KiB  
Article
In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation
by Mats Martinell, Tanja Andersson, Steinar Smørholm Mannsverk, Julia Bergholm, Patrik Ellström, Anna Hill, Johan Lindh and Rene Kaden
Viruses 2022, 14(3), 504; https://doi.org/10.3390/v14030504 - 28 Feb 2022
Cited by 2 | Viewed by 2540
Abstract
We describe a flight-associated infection scenario of seven individuals with a B.1.617.2 (Delta) lineage, harbouring an S:E484Q point mutation. In Sweden, at least 10% of all positive SARS-CoV-2 samples were sequenced in each county; the B.1.717.2 + S:E484Q combination was not detected in [...] Read more.
We describe a flight-associated infection scenario of seven individuals with a B.1.617.2 (Delta) lineage, harbouring an S:E484Q point mutation. In Sweden, at least 10% of all positive SARS-CoV-2 samples were sequenced in each county; the B.1.717.2 + S:E484Q combination was not detected in Sweden before and was imported within the scenario described in this report. The high transmission rate of the delta lineage combined with the S:E484Q mutation, associated with immune escape in other lineages, makes this specific genetic combination a possible threat to the global fight against the COVID-19 pandemic. Even within the Omicron wave, the B.1.617.2 + S:E484Q variant appeared in community samples in Sweden, as it seems that this combination has an evolutionary gain compared to other B.1.617.2 lineages. The here described genomic combination was not detectable with the common fasta file-based Pango-lineage analysis, hence increasing the probability of the true global prevalence to be higher. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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Review

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21 pages, 2127 KiB  
Review
Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era
by Ted Ling-Hu, Estefany Rios-Guzman, Ramon Lorenzo-Redondo, Egon A. Ozer and Judd F. Hultquist
Viruses 2022, 14(11), 2532; https://doi.org/10.3390/v14112532 - 16 Nov 2022
Cited by 10 | Viewed by 3309
Abstract
Global SARS-CoV-2 genomic surveillance efforts have provided critical data on the ongoing evolution of the virus to inform best practices in clinical care and public health throughout the pandemic. Impactful genomic surveillance strategies generally follow a multi-disciplinary pipeline involving clinical sample collection, viral [...] Read more.
Global SARS-CoV-2 genomic surveillance efforts have provided critical data on the ongoing evolution of the virus to inform best practices in clinical care and public health throughout the pandemic. Impactful genomic surveillance strategies generally follow a multi-disciplinary pipeline involving clinical sample collection, viral genotyping, metadata linkage, data reporting, and public health responses. Unfortunately, current limitations in each of these steps have compromised the overall effectiveness of these strategies. Biases from convenience-based sampling methods can obfuscate the true distribution of circulating variants. The lack of standardization in genotyping strategies and bioinformatic expertise can create bottlenecks in data processing and complicate interpretation. Limitations and inconsistencies in clinical and demographic data collection and sharing can slow the compilation and limit the utility of comprehensive datasets. This likewise can complicate data reporting, restricting the availability of timely data. Finally, gaps and delays in the implementation of genomic surveillance data in the public health sphere can prevent officials from formulating effective mitigation strategies to prevent outbreaks. In this review, we outline current SARS-CoV-2 global genomic surveillance methods and assess roadblocks at each step of the pipeline to identify potential solutions. Evaluating the current obstacles that impede effective surveillance can improve both global coordination efforts and pandemic preparedness for future outbreaks. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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Other

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2 pages, 194 KiB  
Correction
Correction: Martínez-Murcia et al. SARS-CoV-2 Variants Identification; A Fast and Affordable Strategy Based on Partial S-Gene Targeted PCR Sequencing. Viruses 2022, 14, 2588
by Antonio Martínez-Murcia, Adrian Garcia-Sirera, Aaron Navarro and Laura Pérez
Viruses 2023, 15(3), 771; https://doi.org/10.3390/v15030771 - 17 Mar 2023
Viewed by 590
Abstract
In the original publication [...] Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
6 pages, 791 KiB  
Brief Report
Structural Insight into the Resistance of the SARS-CoV-2 Omicron BA.4 and BA.5 Variants to Cilgavimab
by Shigeru Fujita, Yusuke Kosugi, Izumi Kimura, Daichi Yamasoba, The Genotype to Phenotype Japan (G2P-Japan) Consortium and Kei Sato
Viruses 2022, 14(12), 2677; https://doi.org/10.3390/v14122677 - 29 Nov 2022
Cited by 4 | Viewed by 1606
Abstract
We have recently revealed that the new SARS-CoV-2 Omicron sublineages BA.4 and BA.5 exhibit increased resistance to cilgavimab, a therapeutic monoclonal antibody, and the resistance to cilgavimab is attributed to the spike L452R substitution. However, it remains unclear how the spike L452R substitution [...] Read more.
We have recently revealed that the new SARS-CoV-2 Omicron sublineages BA.4 and BA.5 exhibit increased resistance to cilgavimab, a therapeutic monoclonal antibody, and the resistance to cilgavimab is attributed to the spike L452R substitution. However, it remains unclear how the spike L452R substitution renders resistance to cilgavimab. Here, we demonstrated that the increased resistance to cilgavimab of the spike L452R is possibly caused by the steric hindrance between cilgavimab and its binding interface on the spike. Our results suggest the importance of developing therapeutic antibodies that target SARS-CoV-2 variants harboring the spike L452R substitution. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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Study Protocol
CovDif, a Tool to Visualize the Conservation between SARS-CoV-2 Genomes and Variants
by Luis F. Cedeño-Pérez and Laura Gómez-Romero
Viruses 2022, 14(3), 561; https://doi.org/10.3390/v14030561 - 09 Mar 2022
Cited by 1 | Viewed by 2199
Abstract
The spread of the newly emerged severe acute respiratory syndrome (SARS-CoV-2) virus has led to more than 430 million confirmed cases, including more than 5.9 million deaths, reported worldwide as of 24 February 2022. Conservation of viral genomes is important for pathogen identification [...] Read more.
The spread of the newly emerged severe acute respiratory syndrome (SARS-CoV-2) virus has led to more than 430 million confirmed cases, including more than 5.9 million deaths, reported worldwide as of 24 February 2022. Conservation of viral genomes is important for pathogen identification and diagnosis, therapeutics development and epidemiological surveillance to detect the emergence of new viral variants. An intense surveillance of virus variants has led to the identification of Variants of Interest and Variants of Concern. Although these classifications dynamically change as the pandemic evolves, they have been useful to guide public health efforts on containment and mitigation. In this work, we present CovDif, a tool to detect conserved regions between groups of viral genomes. CovDif creates a conservation landscape for each group of genomes of interest and a differential landscape able to highlight differences in the conservation level between groups. CovDif is able to identify loss in conservation due to point mutations, deletions, inversions and chromosomal rearrangements. In this work, we applied CovDif to SARS-CoV-2 clades (G, GH, GR, GV, L, O, S and G) and variants. We identified all regions for any defining SNPs. We also applied CovDif to a group of population genomes and evaluated the conservation of primer regions for current SARS-CoV-2 detection and diagnostic protocols. We found that some of these protocols should be applied with caution as few of the primer-template regions are no longer conserved in some SARS-CoV-2 variants. We conclude that CovDif is a tool that could be widely applied to study the conservation of any group of viral genomes as long as whole genomes exist. Full article
(This article belongs to the Special Issue SARS-CoV-2 Genomics)
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