Genomic Epidemiology of SARS-CoV-2 in Pakistan
Tài liệu tham khảo
Umer, 2019, Effects of socio-environmental factors on malaria infection in Pakistan: a Bayesian spatial analysis, Int J Environ Res Public Health, 16, 1365, 10.3390/ijerph16081365
Qi, 2014, Socio-environmental drivers and suicide in Australia: Bayesian spatial analysis, BMC Public Health, 14, 681, 10.1186/1471-2458-14-681
Abid, 2020, Progress of COVID-19 epidemic in Pakistan, Asia Pac J Public Health, 32, 154, 10.1177/1010539520927259
Ghanchi NK, Masood KI, Nasir A, Khan W, Abidi SH, Shahid S, et al. SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic. bioRxiv 2020;234153.
Sayers EW, Beck J, Brister JR, Bolton EE, Canese K, Comeau DC, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2021;49:D10–7.
Zhao, 2020, The 2019 novel coronavirus resource, Yi Chuan, 42, 212
Shakeel M, Irfan M, Zaibunnisa, Rashid M, Ansari SK, Khan IA. Surveillance of genetic diversity and evolution in locally transmitted SARS-CoV-2 in Pakistan during the first wave of the COVID-19 pandemic. bioRxiv 2021;426548.
Song, 2020, The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR, Genomics Proteomics Bioinformatics, 18, 749, 10.1016/j.gpb.2020.09.001
Plante, 2021, Spike mutation D614G alters SARS-CoV-2 fitness, Nature, 592, 116, 10.1038/s41586-020-2895-3
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, et al. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell 2020;182:812–27.e19.
Tang, 2021, Evolutionary analysis and lineage designation of SARS-CoV-2 genomes, Sci Bull (Beijing), 66, 2297, 10.1016/j.scib.2021.02.012
Rambaut, 2020, A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology, Nat Microbiol, 5, 1403, 10.1038/s41564-020-0770-5
Liu, 2020, Population genetics of SARS-CoV-2: disentangling effects of sampling bias and infection clusters, Genomics Proteomics Bioinformatics, 18, 640, 10.1016/j.gpb.2020.06.001
Phillips, 2008, Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems, Nat Rev Genet, 9, 855, 10.1038/nrg2452
Zeng, 2020, Global analysis of more than 50,000 SARS-CoV-2 genomes reveals epistasis between eight viral genes, Proc Natl Acad Sci U S A, 117, 31519, 10.1073/pnas.2012331117
Xu, 2020, Dynamics of severe acute respiratory syndrome coronavirus 2 genome variants in the feces during convalescence, J Genet Genomics, 47, 610, 10.1016/j.jgg.2020.10.002
Shen Z, Xiao Y, Kang L, Ma W, Shi L, Zhang L, et al. Genomic diversity of severe acute respiratory syndrome-coronavirus 2 in patients with coronavirus disease 2019. Clin Infect Dis 2020;71:713–20.
Choi, 2020, Persistence and evolution of SARS-CoV-2 in an immunocompromised host, N Engl J Med, 383, 2291, 10.1056/NEJMc2031364
Kemp SA, Collier DA, Datir R, Ferreira I, Gayed S, Jahun A, et al. Neutralising antibodies in spike mediated SARS-CoV-2 adaptation. medRxiv 2020;2020.12.05.20241927.
Tang X, Wu C, Li X, Song Y, Yao X, Wu X, et al. On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev 2020;7:1012–23.
Wei X, Li X, Cui J. Evolutionary perspectives on novel coronaviruses identified in pneumonia cases in China. Natl Sci Rev 2020;7:239–42.
Waltenburg, 2021, Coronavirus disease among workers in food processing, food manufacturing, and agriculture workplaces, Emerg Infect Dis, 27, 243, 10.3201/eid2701.203821
James, 2020, High COVID-19 attack rate among attendees at events at a church — Arkansas, March 2020, MMWR Morb Mortal Wkly Rep, 69, 632, 10.15585/mmwr.mm6920e2
Baggett, 2020, Prevalence of SARS-CoV-2 infection in residents of a large homeless shelter in Boston, JAMA, 323, 2191, 10.1001/jama.2020.6887
Khan, 2021, SARS-CoV-2 nucleocapsid and Nsp3 binding: an in silico study, Arch Microbiol, 203, 59, 10.1007/s00203-020-01998-6
Lemieux JE, Siddle KJ, Shaw BM, Loreth C, Schaffner SF, Gladden-Young A, et al. Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science 2021;371:eabe3261.
Liu, 2020, Cold-chain transportation in the frozen food industry may have caused a recurrence of COVID-19 cases in destination: successful isolation of SARS-CoV-2 virus from the imported frozen cod package surface, Biosaf Health, 2, 199, 10.1016/j.bsheal.2020.11.003
World Health Organization. Coronavirus disease (COVID-19) technical guidance: surveillance and case definitions. [Internet]. Geneva, Switzerland: World Health Organization; 2020, https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/surveillance-and-case-definitions.
Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill 2020;25:2000045.
Martin, 2011, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet J, 17, 10, 10.14806/ej.17.1.200
Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324
Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352
McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, 20, 1297, 10.1101/gr.107524.110
McLaren, 2016, The Ensembl Variant Effect Predictor, Genome Biol, 17, 122, 10.1186/s13059-016-0974-4
Elbe, 2017, Data, disease and diplomacy: GISAID’s innovative contribution to global health, Glob Chall, 1, 33, 10.1002/gch2.1018
Shu, 2017, GISAID: global initiative on sharing all influenza data — from vision to reality, Euro Surveill, 22, 30494, 10.2807/1560-7917.ES.2017.22.13.30494
Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res 2019;47:W636–41.
Wu, 2020, A new coronavirus associated with human respiratory disease in China, Nature, 579, 265, 10.1038/s41586-020-2008-3
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020;37:1530–4.
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015;32:268–74.
Chen, 2021, The Genome Sequence Archive family: toward explosive data growth and diverse data types, Genomics Proteomics Bioinformatics, 19, 578, 10.1016/j.gpb.2021.08.001
Chen, 2021, Genome Warehouse: a public repository housing genome-scale data, Genomics Proteomics Bioinformatics, 19, 584, 10.1016/j.gpb.2021.04.001
2021, Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2021, Nucleic Acids Res, 49, D18, 10.1093/nar/gkaa1022