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Global disparities in SARS-CoV-2 genomic surveillance.
Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C; Danish Covid-19 Genome Consortium; COVID-19 Impact Project; Network for Genomic Surveillance in South Africa (NGS-SA); GISAID core curation team; Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Brito AF, et al. Among authors: de oliveira t. medRxiv [Preprint]. 2021 Dec 9:2021.08.21.21262393. doi: 10.1101/2021.08.21.21262393. medRxiv. 2021. PMID: 34462754 Free PMC article. Updated. Preprint.
Zika virus complete genome from Salvador, Bahia, Brazil.
Giovanetti M, Faria NR, Nunes MRT, de Vasconcelos JM, Lourenço J, Rodrigues SG, Vianez JL Jr, da Silva SP, Lemos PS, Tavares FN, Martin DP, do Rosário MS, Siqueira IC, Ciccozzi M, Pybus OG, de Oliveira T, Alcantara LC Junior. Giovanetti M, et al. Among authors: de oliveira t, de vasconcelos jm. Infect Genet Evol. 2016 Jul;41:142-145. doi: 10.1016/j.meegid.2016.03.030. Epub 2016 Apr 9. Infect Genet Evol. 2016. PMID: 27071531
Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study.
Kraemer MUG, Faria NR, Reiner RC Jr, Golding N, Nikolay B, Stasse S, Johansson MA, Salje H, Faye O, Wint GRW, Niedrig M, Shearer FM, Hill SC, Thompson RN, Bisanzio D, Taveira N, Nax HH, Pradelski BSR, Nsoesie EO, Murphy NR, Bogoch II, Khan K, Brownstein JS, Tatem AJ, de Oliveira T, Smith DL, Sall AA, Pybus OG, Hay SI, Cauchemez S. Kraemer MUG, et al. Among authors: de oliveira t. Lancet Infect Dis. 2017 Mar;17(3):330-338. doi: 10.1016/S1473-3099(16)30513-8. Epub 2016 Dec 23. Lancet Infect Dis. 2017. PMID: 28017559 Free PMC article.
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes.
Fonseca V, Libin PJK, Theys K, Faria NR, Nunes MRT, Restovic MI, Freire M, Giovanetti M, Cuypers L, Nowé A, Abecasis A, Deforche K, Santiago GA, Siqueira IC, San EJ, Machado KCB, Azevedo V, Filippis AMB, Cunha RVD, Pybus OG, Vandamme AM, Alcantara LCJ, de Oliveira T. Fonseca V, et al. Among authors: de oliveira t. PLoS Negl Trop Dis. 2019 May 8;13(5):e0007231. doi: 10.1371/journal.pntd.0007231. eCollection 2019 May. PLoS Negl Trop Dis. 2019. PMID: 31067235 Free PMC article.
Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region.
Giovanetti M, Faria NR, Lourenço J, Goes de Jesus J, Xavier J, Claro IM, Kraemer MUG, Fonseca V, Dellicour S, Thézé J, da Silva Salles F, Gräf T, Silveira PP, do Nascimento VA, Costa de Souza V, de Melo Iani FC, Castilho-Martins EA, Cruz LN, Wallau G, Fabri A, Levy F, Quick J, de Azevedo V, Aguiar RS, de Oliveira T, Bôtto de Menezes C, da Costa Castilho M, Terra TM, Souza da Silva M, Bispo de Filippis AM, Luiz de Abreu A, Oliveira WK, Croda J, Campelo de Albuquerque CF, Nunes MRT, Sabino EC, Loman N, Naveca FG, Pybus OG, Alcantara LC. Giovanetti M, et al. Among authors: de melo iani fc, oliveira wk, de oliveira t, de azevedo v. Cell Rep. 2020 Feb 18;30(7):2275-2283.e7. doi: 10.1016/j.celrep.2020.01.085. Cell Rep. 2020. PMID: 32075736 Free article.
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M. Mavian C, et al. Among authors: de oliveira t. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12522-12523. doi: 10.1073/pnas.2007295117. Epub 2020 May 7. Proc Natl Acad Sci U S A. 2020. PMID: 32381734 Free PMC article. No abstract available.
Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report.
Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenco J, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LC, Petruccione F, de Oliveira T. Giandhari J, et al. Among authors: de oliveira t. medRxiv [Preprint]. 2020 May 29:2020.05.29.20116376. doi: 10.1101/2020.05.29.20116376. medRxiv. 2020. PMID: 32511505 Free PMC article. Updated. Preprint.
Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic.
Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Moosa Y, Mattison S, Gazy I, Fish M, Singh L, Khanyile KS, San JE, Fonseca V, Giovanetti M, Alcantara LC Jr, de Oliveira T. Pillay S, et al. Among authors: de oliveira t. Genes (Basel). 2020 Aug 17;11(8):949. doi: 10.3390/genes11080949. Genes (Basel). 2020. PMID: 32824573 Free PMC article.
970 results