Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020;395(10223):497–506. https://doi.org/10.1016/S0140-6736(20)30183-5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Johns Hopkins Coronavirus Resource Center. COVID-19 Map. Johns Hopkins Coronavirus Resource Center. 2021. https://coronavirus.jhu.edu/map.html. Accessed 10 Nov 2020.
Shu Y, McCauley J. GISAID: global initiative on sharing all influenza data – from vision to reality. Eurosurveillance. 2017;22(13). https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494.
Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria N, et al. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into northern California. Science. 2020;369(6503):582–7. https://doi.org/10.1126/science.abb9263.
Article
CAS
PubMed
Google Scholar
Fauver JR, Petrone ME, Hodcroft EB, Shioda K, Ehrlich HY, Watts AG, et al. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell. 2020;181:990–6 e5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ladner JT, Larsen BB, Bowers JR, Hepp CM, Bolyen E, Folkerts M, et al. An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona. mBio. 2020;11. https://doi.org/10.1128/mBio.02107-20.
Maurano MT, Ramaswami S, Zappile P, Dimartino D, Boytard L, Ribeiro-dos-Santos AM, et al. Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region. Genome Res. 2020;30:1781–88. https://doi.org/10.1101/gr.266676.120.
Bartolini B, Rueca M, Gruber CEM, Messina F, Carletti F, Giombini E, et al. SARS-CoV-2 phylogenetic analysis, Lazio region, Italy, February–march 2020. Emerg Infect Dis. 2020;26(8):1842–5. https://doi.org/10.3201/eid2608.201525.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oude Munnink BB, Nieuwenhuijse DF, Stein M, O’Toole Á, Haverkate M, Mollers M, et al. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nat Med. 2020;26(9):1405–10. https://doi.org/10.1038/s41591-020-0997-y.
Article
CAS
PubMed
Google Scholar
Rockett RJ, Arnott A, Lam C, Sadsad R, Timms V, Gray K-A, et al. Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nat Med. 2020;26:1398–1404. https://doi.org/10.1038/s41591-020-1000-7.
Seemann T, Lane CR, Sherry NL, Duchene S, Gonçalves da Silva A, Caly L, et al. Tracking the COVID-19 pandemic in Australia using genomics. Nat Commun. 2020;11:4376.
Article
CAS
PubMed
PubMed Central
Google Scholar
Candido D, Claro IM, de Jesus JG, Souza WM, Moreira FRR, Dellicour S, et al. Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science. 2020;369(6508):1255–60. https://doi.org/10.1126/science.abd2161.
Article
CAS
PubMed
Google Scholar
Paiva MHS, Guedes DRD, Docena C, Bezerra MF, Dezordi FZ, Machado LC, et al. Multiple introductions followed by ongoing community spread of SARS-CoV-2 at one of the largest metropolitan areas of Northeast Brazil. Viruses. 2020;12(12):1414. https://doi.org/10.3390/v12121414.
Article
CAS
PubMed Central
Google Scholar
Xavier J, Giovanetti M, Adelino T, Fonseca V, da Costa AVB, Ribeiro AA, et al. The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing. Emerg Microbes Infect. 2020;9(1):1824–34. https://doi.org/10.1080/22221751.2020.1803146.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403–7. https://doi.org/10.1038/s41564-020-0770-5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takahiko Koyama, Daniel Platt, Laxmi Parida. WHO | Variant analysis of SARS-CoV-2 genomes. https://www.who.int/bulletin/volumes/98/7/20-253591/en/. Accessed 24 Nov 2020.
Laamarti M, Alouane T, Kartti S, Chemao-Elfihri MW, Hakmi M, Essabbar A, et al. Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. PLoS One. 2020;15(11):e0240345. https://doi.org/10.1371/journal.pone.0240345.
Article
CAS
PubMed
PubMed Central
Google Scholar
van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, et al. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infect Genet Evol. 2020;83:104351. https://doi.org/10.1016/j.meegid.2020.104351.
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(4):812–827.e19. https://doi.org/10.1016/j.cell.2020.06.043.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li Q, Wu J, Nie J, Zhang L, Hao H, Liu S, et al. The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Cell. 2020;182:1284–94 e9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Toyoshima Y, Nemoto K, Matsumoto S, Nakamura Y, Kiyotani K. SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. J Hum Genet. 2020;65(12):1075–82. https://doi.org/10.1038/s10038-020-0808-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Volz E, Hill V, McCrone JT, Price A, Jorgensen D, O’Toole Á, et al. Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity. Cell. 2020;184(1):64–75.e11. https://doi.org/10.1016/j.cell.2020.11.020.
Article
CAS
PubMed
Google Scholar
Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature. 2021;592:116–21. https://doi.org/10.1038/s41586-020-2895-3.
Gu H, Chen Q, Yang G, He L, Fan H, Deng Y-Q, et al. Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. Science. 2020;369(6511):1603–7. https://doi.org/10.1126/science.abc4730.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baum A, Fulton BO, Wloga E, Copin R, Pascal KE, Russo V, et al. Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science. 2020;369(6506):1014–8. https://doi.org/10.1126/science.abd0831.
Article
CAS
PubMed
Google Scholar
Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, et al. Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Cell Host Microbe. 2020;29(1):44–57.e9. https://doi.org/10.1016/j.chom.2020.11.007.
Article
CAS
PubMed
Google Scholar
Weisblum Y, Schmidt F, Zhang F, DaSilva J, Poston D, Lorenzi JC, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. eLife. 2020;9:e61312. https://doi.org/10.7554/eLife.61312.
Article
CAS
PubMed
PubMed Central
Google Scholar
Calcagno A, Ghisetti V, Burdino E, Trunfio M, Allice T, Boglione L, et al. Coinfection with other respiratory pathogens in COVID-19 patients. Clin Microbiol Infect. 2020;0. https://doi.org/10.1016/j.cmi.2020.08.012.
Kim D, Quinn J, Pinsky B, Shah NH, Brown I. Rates of co-infection between SARS-CoV-2 and other respiratory pathogens. JAMA. 2020;323(20):2085–6. https://doi.org/10.1001/jama.2020.6266.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nowak MD, Sordillo EM, Gitman MR, Mondolfi AEP. Coinfection in SARS-CoV-2 infected patients: where are influenza virus and rhinovirus/enterovirus? J Med Virol. 2020;92(10):1699–700. https://doi.org/10.1002/jmv.25953.
Article
CAS
PubMed
Google Scholar
Peddu V, Shean RC, Xie H, Shrestha L, Perchetti GA, Minot SS, et al. Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization. Clin Chem. 2020;66(7):966–72. https://doi.org/10.1093/clinchem/hvaa106.
Article
PubMed
Google Scholar
Zhang Q, Bastard P, Liu Z, Le Pen J, Moncada-Velez M, Chen J, et al. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science. 2020;370(6515):eabd4570. https://doi.org/10.1126/science.abd4570.
Article
PubMed
PubMed Central
Google Scholar
Hou Y, Zhao J, Martin W, Kallianpur A, Chung MK, Jehi L, et al. New insights into genetic susceptibility of COVID-19: an ACE2 and TMPRSS2 polymorphism analysis. BMC Med. 2020;18(1):216. https://doi.org/10.1186/s12916-020-01673-z.
Article
CAS
PubMed
PubMed Central
Google Scholar
Choudhary S, Sreenivasulu K, Mitra P, Misra S, Sharma P. Role of genetic variants and gene expression in the susceptibility and severity of COVID-19. Ann Lab Med. 2021;41(2):129–38. https://doi.org/10.3343/alm.2021.41.2.129.
Article
PubMed
PubMed Central
Google Scholar
De La Cruz M, Nunes DP, Bhardwaj V, Subramanyan D, Zaworski C, Roy P, et al. Colonic epithelial angiotensin-converting enzyme 2 (ACE2) expression in blacks and whites: potential implications for pathogenesis Covid-19 racial disparities. J Racial Ethn Health Disparities. 2021. https://doi.org/10.1007/s40615-021-01004-9.
Guilger-Casagrande M, de Barros CT, Antunes VAN, de Araujo DR, Lima R. Perspectives and challenges in the fight against COVID-19: the role of genetic variability. Front Cell Infect Microbiol. 2021;11. https://doi.org/10.3389/fcimb.2021.598875.
Trump S, Lukassen S, Anker MS, Chua RL, Liebig J, Thürmann L, et al. Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19. Nat Biotechnol. 2020:1–12. https://doi.org/10.1038/s41587-020-00796-1.
Secolin R, de Araujo TK, Gonsales MC, Rocha CS, Naslavsky M, Marco LD, et al. Genetic variability in COVID-19-related genes in the Brazilian population. Hum Genome Var. 2021;8:1–9.
Article
Google Scholar
Rio Grande do Sul Department of Health. SES-RS - Coronavírus. https://ti.saude.rs.gov.br/covid19/. Accessed 24 Nov 2020.
Brazilian Institute of Geography and Statistics - IBGE. Cidades e Estados: Rio Grande do Sul. https://www.ibge.gov.br/cidades-e-estados/rs.html. Accessed 24 Nov 2020.
Esteio Department of Health. Monitoramento COVID-19 Esteio. http://covid.esteio.rs.gov.br/. Accessed 24 Nov 2020.
Petersen E, Koopmans M, Go U, Hamer DH, Petrosillo N, Castelli F, et al. Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics. Lancet Infect Dis. 2020;20(9):e238–44. https://doi.org/10.1016/S1473-3099(20)30484-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang W, Kandula S, Huynh M, Greene SK, Wye GV, Li W, et al. Estimating the infection-fatality risk of SARS-CoV-2 in New York City during the spring 2020 pandemic wave: a model-based analysis. Lancet Infect Dis. 2021;21(2):203–12. https://doi.org/10.1016/S1473-3099(20)30769-6.
Article
CAS
PubMed
Google Scholar
Secolin R, Gonsales MC, Rocha CS, Naslavsky M, De Marco L, Bicalho MAC, et al. Exploring a Region on Chromosome 8p23.1 Displaying Positive Selection Signals in Brazilian Admixed Populations: Additional Insights Into Predisposition to Obesity and Related Disorders. Front Genet. 2021;12. https://doi.org/10.3389/fgene.2021.636542.
Walls AC, Park Y-J, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell. 2020;181:281–92 e6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seyran M, Takayama K, Uversky VN, Lundstrom K, Palù G, Sherchan SP, et al. The structural basis of accelerated host cell entry by SARS-CoV-2. FEBS J. 2020. https://doi.org/10.1111/febs.15651.
Mansbach RA, Chakraborty S, Nguyen K, Montefiori DC, Korber B, Gnanakaran S. The SARS-CoV-2 Spike variant D614G favors an open conformational state. Sci Adv. 2021;7:eabf3671. https://doi.org/10.1126/sciadv.abf3671.
Singer J, Gifford R, Cotten M, Robertson D. CoV-GLUE: A Web Application for Tracking SARS-CoV-2 Genomic Variation. 2020. https://doi.org/10.20944/preprints202006.0225.v1.
Forni D, Filippi G, Cagliani R, De Gioia L, Pozzoli U, Al-Daghri N, et al. The heptad repeat region is a major selection target in MERS-CoV and related coronaviruses. Sci Rep. 2015;5(1):14480. https://doi.org/10.1038/srep14480.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature. 2021;592:438–43. https://doi.org/10.1038/s41586-021-03402-9.
Ferrareze PAG, Franceschi VB, de Menezes Mayer A, Caldana GD, Zimerman RA, Thompson CE. E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. bioRxiv. 2021; 2021.01.27.426895. https://doi.org/10.1101/2021.01.27.426895.
Nonaka CKV, Franco MM, Gräf T, Barcia CA de L, Mendonça RN de Á, Sousa KAF de, et al. Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil. Emerg Infect Dis. 2021;27:1522. https://doi.org/10.3201/eid2705.210191.
Voloch CM, Francisco R da S, Almeida LGP de, Cardoso CC, Brustolini OJ, Gerber AL, et al. Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil. J Virol. 2021;95. https://doi.org/10.1128/JVI.00119-21.
Nelson G, Buzko O, Spilman P, Niazi K, Rabizadeh S, Soon-Shiong P. Molecular dynamic simulation reveals E484K mutation enhances spike RBD-ACE2 affinity and the combination of E484K, K417N and N501Y mutations (501Y.V2 variant) induces conformational change greater than N501Y mutant alone, potentially resulting in an escape mutant. bioRxiv. 2021; 2021.01.13.426558. https://doi.org/10.1101/2021.01.13.426558.
Faria N, Claro IM, Candido D, Franco LAM, Andrade PS, Coletti TM, et al. Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings. Virological. 2021; https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586. Accessed 14 Jan 2021.
Lei X, Dong X, Ma R, Wang W, Xiao X, Tian Z, et al. Activation and evasion of type I interferon responses by SARS-CoV-2. Nat Commun. 2020;11(1):3810. https://doi.org/10.1038/s41467-020-17665-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schultze JL, Aschenbrenner AC. COVID-19 and the human innate immune system. Cell. 2021;184(7):1671–92. https://doi.org/10.1016/j.cell.2021.02.029.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chang C, Hou M-H, Chang C-F, Hsiao C-D, Huang T. The SARS coronavirus nucleocapsid protein--forms and functions. Antivir Res. 2014;103:39–50. https://doi.org/10.1016/j.antiviral.2013.12.009.
Article
CAS
PubMed
Google Scholar
Verheije MH, Hagemeijer MC, Ulasli M, Reggiori F, Rottier PJM, Masters PS, et al. The coronavirus Nucleocapsid protein is dynamically associated with the replication-transcription complexes. J Virol. 2010;84(21):11575–9. https://doi.org/10.1128/JVI.00569-10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Velasco JM, Chinnawirotpisan P, Joonlasak K, Manasatienkij W, Huang A, Valderama MT, et al. Coding-complete genome sequences of 23 SARS-CoV-2 samples from the Philippines. Microbiol Resour Announc. 2020;9(43). https://doi.org/10.1128/MRA.01031-20.
Franco-Muñoz C, Álvarez-Díaz DA, Laiton-Donato K, Wiesner M, Escandón P, Usme-Ciro JA, et al. Substitutions in spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. Infect Genet Evol. 2020;85:104557. https://doi.org/10.1016/j.meegid.2020.104557.
Article
CAS
PubMed
PubMed Central
Google Scholar
Singh J, Singh H, Hasnain SE, Rahman SA. Mutational signatures in countries affected by SARS-CoV-2: Implications in host-pathogen interactome. bioRxiv. 2020; 2020.09.17.301614. https://doi.org/10.1101/2020.09.17.301614.
Villoutreix BO, Calvez V, Marcelin A-G, Khatib A-M. In Silico investigation of the new UK (B.1.1.7) and south African (501Y.V2) SARS-CoV-2 variants with a focus at the ACE2-spike RBD Interface. Int J Mol Sci. 2021;22(4). https://doi.org/10.3390/ijms22041695.
Radzikowska U, Ding M, Tan G, Zhakparov D, Peng Y, Wawrzyniak P, et al. Distribution of ACE2, CD147, CD26, and other SARS-CoV-2 associated molecules in tissues and immune cells in health and in asthma, COPD, obesity, hypertension, and COVID-19 risk factors. Allergy. 2020;75(11):2829–45. https://doi.org/10.1111/all.14429.
Article
CAS
PubMed
Google Scholar
Kehdy FSG, Gouveia MH, Machado M, Magalhães WCS, Horimoto AR, Horta BL, et al. Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations. Proc Natl Acad Sci. 2015;112(28):8696–701. https://doi.org/10.1073/pnas.1504447112.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lima-Costa MF, Rodrigues LC, Barreto ML, Gouveia M, Horta BL, Mambrini J, et al. Genomic ancestry and ethnoracial self-classification based on 5,871 community-dwelling Brazilians (the Epigen initiative). Sci Rep. 2015;5(1):9812. https://doi.org/10.1038/srep09812.
Article
CAS
PubMed
PubMed Central
Google Scholar
de Moura RR, Coelho AVC, de Queiroz Balbino V, Crovella S, Brandão LAC. Meta-analysis of Brazilian genetic admixture and comparison with other Latin America countries. Am J Hum Biol. 2015;27(5):674–80. https://doi.org/10.1002/ajhb.22714.
Article
PubMed
Google Scholar
Feng Y, Ling Y, Bai T, Xie Y, Huang J, Li J, et al. COVID-19 with different severities: a multicenter study of clinical features. Am J Respir Crit Care Med. 2020;201(11):1380–8. https://doi.org/10.1164/rccm.202002-0445OC.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bastos LS, Niquini RP, Lana RM, Villela DAM, Cruz OG, Coelho FC, et al. COVID-19 e hospitalizações por SRAG no Brasil: uma comparação até a 12a semana epidemiológica de 2020. Cad Saúde Pública. 2020;36(4):e00070120. https://doi.org/10.1590/0102-311x00070120.
Article
PubMed
Google Scholar
Alves THE, Souza TA de, Samyla de Almeida Silva, Ramos NA, SV de Oliveira. Underreporting of death by COVID-19 in Brazil’s second Most populous State. Front Public Health 2020;8. doi:https://doi.org/10.3389/fpubh.2020.578645.
Souza CDF de, Paiva JPS de, Leal TC, Silva LF da, Santos LG, Souza CDF de, et al. Spatiotemporal evolution of case fatality rates of COVID-19 in Brazil, 2020. J Bras Pneumol. 2020;46. doi:https://doi.org/10.36416/1806-3756/e20200208.
Mir D, Rego N, Resende PC, López-Tort F, Fernandez-Calero T, Noya V, et al. Recurrent dissemination of SARS-CoV-2 through the Uruguayan-Brazilian border. medRxiv. 2021; 2021.01.06.20249026. https://doi.org/10.1101/2021.01.06.20249026.
Rambaut A, Loman N, Pybus O, Barclay W, Barrett J, Carabelli A, et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological. 2020; https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563. Accessed 4 Jan 2021.
Rambaut A. Phylodynamic analysis | 176 genomes | 6 mar 2020 - SARS-CoV-2 coronavirus / nCoV-2019 genomic epidemiology. Virological. 2020; https://virological.org/t/phylodynamic-analysis-176-genomes-6-mar-2020/356. Accessed 11 Feb 2021.
Su YCF, Anderson DE, Young BE, Linster M, Zhu F, Jayakumar J, et al. Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2. mBio. 2020;11. https://doi.org/10.1128/mBio.01610-20.
Tong KJ, Duchêne DA, Duchêne S, Geoghegan JL, Ho SYW. A comparison of methods for estimating substitution rates from ancient DNA sequence data. BMC Evol Biol. 2018;18(1):70. https://doi.org/10.1186/s12862-018-1192-3.
Article
PubMed
PubMed Central
Google Scholar
Candido D, Watts A, Abade L, Kraemer MUG, Pybus OG, Croda J, et al. Routes for COVID-19 importation in Brazil. J Travel Med. 2020;27(3). https://doi.org/10.1093/jtm/taaa042.
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. Eurosurveillance. 2020;25:2000045.
PubMed Central
Google Scholar
World Health Organization. COVID-19 Clinical management: living guidance. 2021. https://www.who.int/publications-detail-redirect/WHO-2019-nCoV-clinical-2021-1. Accessed 1 May 2021.
Köster J, Rahmann S. Snakemake—a scalable bioinformatics workflow engine. Bioinformatics. 2012;28(19):2520–2. https://doi.org/10.1093/bioinformatics/bts480.
Article
CAS
PubMed
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinforma Oxf Engl. 2014;30(15):2114–20. https://doi.org/10.1093/bioinformatics/btu170.
Article
CAS
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinforma Oxf Engl. 2009;25(14):1754–60. https://doi.org/10.1093/bioinformatics/btp324.
Article
CAS
Google Scholar
Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27(21):2987–93. https://doi.org/10.1093/bioinformatics/btr509.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quinlan AR. BEDTools: the Swiss-Army tool for genome feature analysis. Curr Protoc Bioinforma. 2014;47:11.12.1–34.
Article
Google Scholar
Gel B, Serra E. karyoploteR: an R/bioconductor package to plot customizable genomes displaying arbitrary data. Bioinforma Oxf Engl. 2017;33(19):3088–90. https://doi.org/10.1093/bioinformatics/btx346.
Article
CAS
Google Scholar
Menzel P, Ng KL, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016;7(1):11257. https://doi.org/10.1038/ncomms11257.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wood DE, Lu J, Langmead B. Improved metagenomic analysis with kraken 2. Genome Biol. 2019;20(1):257. https://doi.org/10.1186/s13059-019-1891-0.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a web browser. BMC Bioinformatics. 2011;12(1):385. https://doi.org/10.1186/1471-2105-12-385.
Article
PubMed
PubMed Central
Google Scholar
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. ArXiv12073907 Q-Bio. 2012; http://arxiv.org/abs/1207.3907. Accessed 14 Nov 2020.
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly (Austin). 2012;6(2):80–92. https://doi.org/10.4161/fly.19695.
Article
CAS
Google Scholar
Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;34(23):4121–3. https://doi.org/10.1093/bioinformatics/bty407.
Article
CAS
PubMed
PubMed Central
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80. https://doi.org/10.1093/molbev/mst010.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nguyen L-T, 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(1):268–74. https://doi.org/10.1093/molbev/msu300.
Article
CAS
PubMed
Google Scholar
Tavare S. Some probabilistic and statistical problems in the analysis of DNA sequences. Some Math Quest Biol DNA Seq Anal Ed Robert M Miura 1986. https://agris.fao.org/agris-search/search.do?recordID=US201301755037. Accessed 1 May 2021.
Sagulenko P, Puller V, Neher RA. TreeTime: maximum-likelihood phylodynamic analysis. Virus Evol. 2018;4(1). https://doi.org/10.1093/ve/vex042.
Rambaut A, Lam TT, Max Carvalho L, Pybus OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly path-O-gen). Virus Evol. 2016;2(1). https://doi.org/10.1093/ve/vew007.
Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018;4:vey016.
Article
PubMed
PubMed Central
Google Scholar
Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, et al. BEAGLE: an application programming Interface and high-performance computing library for statistical Phylogenetics. Syst Biol. 2012;61(1):170–3. https://doi.org/10.1093/sysbio/syr100.
Article
PubMed
Google Scholar
Ferreira MAR, Suchard MA. Bayesian analysis of elapsed times in continuous-time Markov chains. Can J Stat. 2008;36(3):355–68. https://doi.org/10.1002/cjs.5550360302.
Article
Google Scholar
Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in Bayesian Phylogenetics using tracer 1.7. Syst Biol. 2018;67(5):901–4. https://doi.org/10.1093/sysbio/syy032.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8:28–36.
Article
Google Scholar
Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian Phylogeography finds its roots. PLoS Comput Biol. 2009;5(9):e1000520. https://doi.org/10.1371/journal.pcbi.1000520.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A, Lemey P. SpreaD3: interactive visualization of spatiotemporal history and trait evolutionary processes. Mol Biol Evol. 2016;33(8):2167–9. https://doi.org/10.1093/molbev/msw082.
Article
CAS
PubMed
PubMed Central
Google Scholar