The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing

References

• World Health Organization (WHO). Novel coronavirus (2019-nCoV) Situation report - 1, 21 January 2020 [Internet]. New York: WHO Bull; 2020; Available from: https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200121-sitrep-1-2019-ncov.pdf?sfvrsn=20a99c10_4.
   Google Scholar
• Lu R, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet; 2020;395:565–574.
   Google Scholar
• Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265–269.
   PubMed Web of Science ®Google Scholar
• Zhu N, Zhang D, Wang W, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382:727–733.
   PubMed Web of Science ®Google Scholar
• Zhou P, Lou YX, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579:270–273.
   PubMed Web of Science ®Google Scholar
• Zhang T, Wu Q, Zhang Z. Pangolin homology associated with 2019-nCoV. bioRxiv. 2020;1:1–23.
   Google Scholar
• Andersen KG, Rambaut A, Lipkin WI, et al. The proximal origin of SARS-CoV-2. Nat Med. 2020;26:450–452.
   PubMed Web of Science ®Google Scholar
• World Health Organization (WHO). Coronavirus disease (COVID-19) Situation Report–165, 3 July 2020 [Internet]. 2020. Available from: https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200703-covid-19-sitrep-165.pdf?sfvrsn=b27a772e_2.
   Google Scholar
• Gorbalenya AE, Baker SC, Baric RS, et al. The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol [Internet]. 2020;5:536–544. doi:10.1038/s41564-020-0695-z.
   PubMed Web of Science ®Google Scholar
• World Health Organization (WHO). Coronavirus disease 2019 (COVID-19). Situation Report – 51 11 March 2020 [Internet]. 2020. Available from: https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200311-sitrep-51-covid-19.pdf?sfvrsn=1ba62e57_10.
   Google Scholar
• Ministério da Saúde. Boletim Epidemiológico Especial-14 / SE 18-26 de abril de 2020 COE-COVID19 [Internet]. 2020. Available from: https://portalarquivos.saude.gov.br/images/pdf/2020/April/27/2020-04-27-18-05h-BEE14-Boletim-do-COE.pdf.
   Google Scholar
• World Health Organization (WHO). Coronavirus disease (COVID-19) Situation Report – 103, 02 May 2020 [Internet]. 2020. Available from: https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200502-covid-19-sitrep-103.pdf?sfvrsn=d95e76d8_4.
   Google Scholar
• Jaqueline Goes de J, Sacchi C, Claro I, et al. First cases of coronavirus disease (COVID-19) in Brazil, South America (2 genomes, 3rd March 2020) [Internet]. Virol. genome reports. 2020. p. 1. Available from: http://virological.org/t/first-cases-of-coronavirus-disease-covid-19-in-brazil-south-america-2-genomes-3rd-march-2020/409.
   Google Scholar
• Instituto Brasileiro de Geografia e Estatística - IBGE. Cidades e Estados: Minas Gerais [Internet]. 2020. Available from: https://www.ibge.gov.br/cidades-e-estados/mg.html.
   Google Scholar
• Gardy JL, Loman NJ. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat Rev Genet. 2018;19:9–20.
   PubMed Web of Science ®Google Scholar
• Quick J. nCoV-2019 sequencing protocol. protocols.io; 2020.
   Google Scholar
• Quick J, Grubaugh ND, Pullan ST, et al. Multiplex PCR method for MinION and Illumina sequencing of zika and other virus genomes directly from clinical samples. Nat Protoc. 2017;12:1261–1276.
   PubMed Web of Science ®Google Scholar
• Cleemput S, Dumon W, Fonseca V, et al. Genome detective coronavirus typing tool for rapid identification and characterization of novel coronavirus genomes. Bioinformatics. 2020;36:3552–3555.
   PubMed Web of Science ®Google Scholar
• Vilsker M, Moosa Y, Nooij S, et al. Genome detective: an automated system for virus identification from high-throughput sequencing data. Bioinformatics. 2019;35:871–873.
   PubMed Web of Science ®Google Scholar
• Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2019;20:1160–1166.
   PubMed Web of Science ®Google Scholar
• Laarson A. Aliview: a fast and lightweight alignment viewer and editor for large data sets. Bioinformatics. 2014;30:3276–3278.
   PubMed Web of Science ®Google Scholar
• Nguyen LT, Schmidt HA, Von Haeseler A, et al. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–274.
   PubMed Web of Science ®Google Scholar
• O’Toole Á, McCrone J. Phylogenetic Assignment of Named Global Outbreak LINeages [Internet]. 2020. Available from: https://github.com/hCoV-2019/pangolin.
   Google Scholar
• Rambaut A, Lam TT, Max Carvalho L, et al. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2:1–7.
   Web of Science ®Google Scholar
• Suchard MA, Lemey P, Baele G, et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018;4:1–16.
   Web of Science ®Google Scholar
• Griffiths RC, Tavaré S. Sampling theory for neutral alleles in a varying environment. Philos Trans R Soc Lond B Biol Sci. 1994;344:403–410.
   PubMed Web of Science ®Google Scholar
• Rambaut A, Drummond AJ, Xie D, et al. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 2018;67:901–904
   PubMed Web of Science ®Google Scholar
• Costa W. Confirmed cases and deaths of COVID-19 in Brazil, at municipal (city) level [Internet]. 2020. Available from: https://github.com/wcota/covid19br.
   Google Scholar
• Ministério da Saúde. Secretaria-Geral da Presidência da República - Imprensa Nacional: Portaria No 188, De 3 De Fevereiro De 2020 [Internet]. Brasília: Diário Of. da União; Available from: http://www.in.gov.br/en/web/dou/-/portaria-n-188-de-3-de-fevereiro-de-2020-241408388.
   Google Scholar
• Secretaria de Estado de Saúde de Minas Gerais. Boletim Epidemiológico COVID-19: Doença causada pelo coronavírus –19 28 de abril de 2020 [Internet]. 2020. Available from: https://saude.mg.gov.br/images/noticias_e_eventos/000_2020/mar_abr_maio/28.04.2020_Boletim_epidemiologico_COVID-19_MG.pdf.
   Google Scholar
• Instituto Brasileiro de Geografia e Estatística - IBGE. Cidades e Estados - Belo Horizonte [Internet]. 2020. Available from: https://www.ibge.gov.br/cidades-e-estados/mg/belo-horizonte.html.
   Google Scholar
• Spychalski P, Błażyńska-Spychalska A, Kobiela J. Estimating case fatality rates of COVID-19. Lancet Infect Dis. 2020;20:774–775.
   PubMedGoogle Scholar
• Russell TW, Hellewell J, Jarvis CI, et al. Estimating the infection and case fatality ratio for coronavirus disease (COVID-19) using age-adjusted data from the outbreak on the Diamond Princess cruise ship, February 2020. Eurosurveillance. 2020;25:1–5.
   Google Scholar
• Verity R, Okell LC, Dorigatti I, et al. Estimates of the severity of coronavirus disease 2019: a model-based analysis. Lancet Infect Dis. 2020;20:669–677.
   PubMed Web of Science ®Google Scholar
• Wu JT, Leung K, Bushman M, et al. Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China. Nat Med. 2020;26:506–510.
   PubMed Web of Science ®Google Scholar
• Flaxman S, Mishra S, Gandy A, et al. Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in 11 European countries. Imp Coll London. 2020.
   Google Scholar
• Wallinga J, Lipsitch M. How generation intervals shape the relationship between growth rates and reproductive numbers. Proc R Soc B Biol Sci. 2007;274:599–604.
   PubMed Web of Science ®Google Scholar
• Moorthy V, Henao M, Preziosi M, et al. Data sharing during the novel coronavirus public health emergency of international concern. Bull World Health Organ [Internet]. New York: 2020: 4–6. Available from: https://www.who.int/bulletin/online_first/20-251561.pdf.
   PubMedGoogle Scholar
• Rambaut A, Holmes EC, Hill V, et al. A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology. bioRxiv. 2020.
   Google Scholar
• Nextstrain. Genomic epidemiology of novel coronavirus - Global subsampling [Internet]. 2020. Available from: https://nextstrain.org/ncov/global?branchLabel=clade&c=clade_membership&r=location&s=Canada/BC_64686/2020.
   Google Scholar
• Munnink BBO, Nieuwenhuijse DF, Stein M, et al. Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands. bioRxiv. 2020.
   Google Scholar
• Lu J, du Plessis L, Liu Z, et al. Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China. Cell [Internet]. 2020 [cited 2020 May 22]; Available from: https://linkinghub.elsevier.com/retrieve/pii/S0092867420304864.
   Google Scholar
• Mavian C, Marini S, Prosperi M, et al. A snapshot of SARS-CoV-2 genome availability up to April 2020 and its implications (Preprint). JMIR Public Heal Surveill [Internet]. 2020 [cited 2020 May 22]; Available from: http://preprints.jmir.org/preprint/19170/accepted.
   Google Scholar
• Mavian C, Marini S, Manes C, et al. Regaining perspective on SARS-CoV-2 molecular tracing and its implications. medRxiv. 2020.
   Google Scholar
• Rambaut A. Phylodynamic Analysis | 176 genomes | 6 Mar 2020 [Internet]. virological.org. 2020. Available from: http://virological.org/t/phylodynamic-analysis-176-genomes-6-mar-2020/356.
   Google Scholar
• Mellan TA, Hoeltgebaum HH, Mishra S, et al. Report 21: Estimating COVID-19 cases and reproduction number in Brazil. medRxiv. 2020: 20096701.
   Google Scholar
• Gonzalez-Reiche AS, Hernandez MM, Sullivan M, et al. Introductions and early spread of SARS-CoV-2 in the New York city area. medRxiv. 2020.
   Google Scholar
• Kucharski AJ, Russell TW, Diamond C, et al. Early dynamics of transmission and control of COVID-19: a mathematical modelling study. Lancet Infect Dis. 2020;20:553–558.
   PubMed Web of Science ®Google Scholar
• Jesus Jd, Sacchi C, Candido DdS, et al. Importation and early local transmission of COVID-19 in Brazil, 2020. Rev Inst Med Trop Sao Paulo. 2020;62:e30.
   PubMed Web of Science ®Google Scholar