ArticleFrontiers in microbiology2021
A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 26 citations in OpenAlex.
- Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022.BMC genomics · 2024Article
- Recombination Events Among SARS-CoV-2 Omicron Subvariants: Impact on Spike Interaction With ACE2 Receptor and Neutralizing Antibodies.Evolutionary bioinformatics online · 2024Article
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- The Highly Conserved Stem-Loop II Motif Is Dispensable for SARS-CoV-2.Journal of virology · 2023Article
- The highly conserved stem-loop II motif is dispensable for SARS-CoV-2.bioRxiv : the preprint server for biology · 2023Article
- A computational map of the human-SARS-CoV-2 protein-RNA interactome predicted at single-nucleotide resolution.NAR genomics and bioinformatics · 2023Article
- State of the art in epitope mapping and opportunities in COVID-19.Future science OA · 2023Review
- Tracking the first SARS-CoV-2 Omicron BA.5.1.3 outbreak in China.Frontiers in microbiology · 2023Article
- Monitoring and tracking the spread of SARS-CoV-2 in Asturias, Spain.Access microbiology · 2023Article
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- Statistical analysis supports UTR (untranslated region) deletion theory in SARS-CoV-2.Virulence · 2022Article
- Investigation of SARS-CoV-2 Variants and Their Effect on SARS-CoV-2 Monoclonal Antibodies, Convalescent and Vaccine Plasma by a Novel Web Tool.Diagnostics (Basel, Switzerland) · 2022Article
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- ORF8 protein of SARS-CoV-2 reduces male fertility in mice.Journal of medical virology · 2022Article
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- Article
- Molecular epidemiology and genetic characterization of SARS-CoV-2 in Kuwait: A descriptive study.Frontiers in microbiology · 2022Article
- Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021.Microbiology resource announcements · 2021Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An unprecedented amount of SARS-CoV-2 sequencing has been performed, however, novel bioinformatic tools to cope with and process these large datasets is needed. Here, we have devised a bioinformatic pipeline that inputs SARS-CoV-2 genome sequencing in FASTA/FASTQ format and outputs a single Variant Calling Format file that can be processed to obtain variant annotations and perform downstream population genetic testing. As proof of concept, we have analyzed over 229,000 SARS-CoV-2 viral sequences up until November 30, 2020. We have identified over 39,000 variants worldwide with increased polymorphisms, spanning the ORF3a gene as well as the 3' untranslated (UTR) regions, specifically in the conserved stem loop region of SARS-CoV-2 which is accumulating greater observed viral diversity relative to chance variation. Our analysis pipeline has also discovered the existence of SARS-CoV-2 hypermutation with low frequency (less than in 2% of genomes) likely arising through host immune responses and not due to sequencing errors. Among annotated non-sense variants with a population frequency over 1%, recurrent inactivation of the ORF8 gene was found. This was found to be present in the newly identified B.1.1.7 SARS-CoV-2 lineage that originated in the United Kingdom. Almost all VOC-containing genomes possess one stop codon in ORF8 gene (Q27
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