References
- Johns Hopkins University & Medicine . Coronavirus Resource Center (2022). https://coronavirus.jhu.edu/map.html
- Drew T . The emergence and evolution of swine viral diseases: to what extent have husbandry systems and global trade contributed to their distribution and diversity?Rev. Sci. Tech.30(1), 95–106 (2011).
- Sharma A , TiwariS , DebMK , MartyJL. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): a global pandemic and treatment strategies. Int. J. Antimicrob. Agents56(2), 106054 (2020).
- Domingo E , MartinV , PeralesC , Grande-PérezA , García-ArriazaJ , AriasA. Viruses as quasispecies: biological implications. Curr. Top. Microbiol. Immunol.299, 51–82 (2006).
- Minskaia E , HertzigT , GorbalenyaAEet al. Discovery of an RNA virus 3’ → 5’ exoribonuclease that is critically involved in coronavirus RNA synthesis. PNAS103(13), 5108–5113 (2006).
- Wan Y . Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. J. Virol.94(7), e00127-20 (2020).
- Ogando S , Zevenhoven-DobbeC , MeerY , BredenbeekJ , PosthumaC , SnijderJ. The enzymatic activity of the Nsp14 exoribonuclease is critical for replication of MERS-CoV and SARS-CoV-2. J. Virol.94(23), e01246-20 (2006).
- Davies G , JarvisI , EdmundsJ , JewellP , Diaz-OrdazK , KeoghH. Increased mortality in community-tested cases of SARS-CoV-2 Lineage B.1.1.7. Nature593, 270–274 (2021).
- Roussel Y , Giraud-GatineauA , JimenoTet al. SARS-CoV-2: fear versus data. Int. J. Antimicrob. Agents55(5), 105947 (2020).
- Hauser A , CounotteJ , MargossianCet al. Estimation of SARS-CoV-2 mortality during the early stages of an epidemic: a modeling study in Hubei, China, and six regions in Europe. PLOS Med.17(7), 1003189 (2020).
- COVID-19 Genomics UK Consortium . Report on SARS-CoV-2 Spike mutations of special interest (2020). www.cogconsortium.uk/wp-content/uploads/2021/01/Report-2_COG-UK_SARS-CoV-2-Mutations.pdf
- Center for Disease Control and Prevention . SARS-CoV-2 variant classifications and definitions (2020). www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html
- Zhu N , ZhangD , WangWet al. China Novel Coronavirus Investigating and Research Team. A novel coronavirus from patients with pneumonia in China. N. Engl. J. Med.382(8), 727–733 (2020).
- Yin C . Genotyping coronavirus SARS-CoV-2: methods and implications. Genomics112(5), 3588–3596 (2020).
- Garcia-Beltran F , LamC , StDenis Ket al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell184(9), 2372–2383 (2021).
- Chen AT , AltschulerK , ZhanH , ChanA , DevermanE. COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. Elife10, e63409 (2021).
- Shu Y , McCauleyJ. GISAID: Global Initiative on Sharing All Influenza Data–from vision to reality. Euro Surveill.22(13), 30494 (2017).
- Esbin N , WhitneyN , ChongS , MaurerA , DarzacqX , TjianR. Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection. RNA26(7), 771–783 (2020).
- Chung NC , MiasojedowB , StartekM , GambinA. Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data. BMC Bioinform.24(20), 644 (2019).
- Zhou P , YangL , WangGet al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature579(7798), 270–273 (2020).
- Metsky C , SiddleJ , Gladden-YoungAet al. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat. Biotechnol.37(2), 160–168 (2019).
- Gohl M , GarbeJ , GradyP , DanielJet al. A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2. BMC Genomics21(1), 863 (2020).
- Grubaugh D , GangavarapuK , QuickJet al. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and IVar. Genome Biol.20(1), 8 (2019).
- The ARTIC Network . Protocols.io. nCoV-2019 sequencing protocol v3 (LoCost) V.3 (2020). www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bp2l6n26rgqe/v3
- Larman B , ScottR , WoganM , OliveiraG , TorkamaniA , SchultzG. Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay. Nucleic Acids Res.42(14), 9146–9157 (2014).
- Credle J , RobinsonL , GunnJet al. Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping. Mod. Pathol.34(6), 1093–1103 (2021).
- Schmid-Burgk L , SchmithausenM , LiDet al. LAMP-Seq: population-scale COVID-19 diagnostics using combinatorial barcoding. bioRxiv025635 (2020).
- Hoff K , DingX , CarterLet al. Highly accurate chip-based resequencing of SARS-CoV-2 clinical samples. Langmuir37(16), 4763–4771 (2021).
- Mockler C , EckerR. Applications of DNA tiling arrays for whole-genome analysis. Genomics85(1), 1–15 (2005).
- Pattabiraman C . Tracking SARS-COV-2 variants of concern. ORF Special Rep.144, (2021).
- Hadfield J et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics34(23), 4121–4123 (2018).
- Bustin A , NolanT. RT-QPCR testing of SARS-CoV-2: a primer. Int. J. Mol. Sci.21(8), 3004 (2020).
- Chen H , BoutrosC. VennDiagram: a package for the generation of highly-customizable Vennn and Eulerr diagrams in R. BMC Bioinformatics12(1), 35 (2011).
- Zenodo . A global phylogeny of SARS-CoV-2 sequences from GISAID (2020). https://zenodo.org/record/4148730#.YvJvny-B30o
- Camacho C , CoulourisG , AvagyanVet al. BLAST+: architecture and applications. BMC Bioinformatics10, 421 (2009).
- Altschul F , GishW , MillerW , MyersW , LipmanJ. Basic local alignment search tool. J. Mol. Biol.215(3), 403–410 (1990).
- Wickham H , NavarroD , PedersenTL. Ggplot2: Elegant Graphics for Data Analysis (Volume 2).Springer, Verlag, New York, USA (2016).
- Nowak A . What is a quasispecies?Trends Ecol. Evol.7(4), 118–121 (1992).
- Jary A , LeducqV , MaletIet al. Evolution of viral quasispecies during SARS-CoV-2 infection. Clin. Microbiol. Infect.26(11), 1560 (2020).