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Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing.
Claro IM, Ramundo MS, Coletti TM, da Silva CAM, Valenca IN, Candido DS, Sales FCS, Manuli ER, de Jesus JG, de Paula A, Felix AC, Andrade PDS, Pinho MC, Souza WM, Amorim MR, Proenca-Modena JL, Kallas EG, Levi JE, Faria NR, Sabino EC, Loman NJ, Quick J. Claro IM, et al. Wellcome Open Res. 2023 Apr 24;6:241. doi: 10.12688/wellcomeopenres.17170.2. eCollection 2021. Wellcome Open Res. 2023. PMID: 37224315 Free PMC article.
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. medRxiv [Preprint]. 2021 Dec 9:2021.08.21.21262393. doi: 10.1101/2021.08.21.21262393. medRxiv. 2021. Update in: Nat Commun. 2022 Nov 16;13(1):7003. doi: 10.1038/s41467-022-33713-y. PMID: 34462754 Free PMC article. Updated. Preprint.
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; Bulgarian SARS-CoV-2 sequencing group; Communicable Diseases Genomics Network (Australia and New Zealand); COVID-19 Impact Project; Danish Covid-19 Genome Consortium; Fiocruz COVID-19 Genomic Surveillance Network; GISAID core curation team; Network for Genomic Surveillance in South Africa (NGS-SA); Swiss SARS-CoV-2 Sequencing Consortium; 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, Branda B, 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. Nat Commun. 2022 Nov 16;13(1):7003. doi: 10.1038/s41467-022-33713-y. Nat Commun. 2022. PMID: 36385137 Free PMC article.
SARS-CoV-2 antibody dynamics in blood donors and COVID-19 epidemiology in eight Brazilian state capitals: A serial cross-sectional study.
Prete CA Jr, Buss LF, Whittaker C, Salomon T, Oikawa MK, Pereira RHM, Moura ICG, Delerino L, Barral-Netto M, Tavares NM, Franca RFO, Boaventura VS, Miyajima F, Mendrone-Junior A, de Almeida-Neto C, Salles NA, Ferreira SC, Fladzinski KA, de Souza LM, Schier LK, Inoue PM, Xabregas LA, Crispim MAE, Fraiji N, Araujo FLV, Carlos LMB, Pessoa V, Ribeiro MA, de Souza RE, da Silva SMN, Cavalcante AF, Valença MIB, da Silva MV, Lopes E, Filho LA, Mateos SOG, Nunes GT, Silva-Junior AL, Busch MP, Castro MC, Dye C, Ratmann O, Faria NR, Nascimento VH, Sabino EC. Prete CA Jr, et al. Elife. 2022 Sep 22;11:e78233. doi: 10.7554/eLife.78233. Elife. 2022. PMID: 36135358 Free PMC article.
Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals.
Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete CA Jr, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro MC, Costa SF, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim DM, Miscouridou X, Mishra S, Monod M, Moreira FRR, Nelson B, Pereira RHM, Ranzani O, Schnekenberg RP, Semenova E, Sonabend R, Souza RP, Xi X, Sabino EC, Faria NR, Bhatt S, Ratmann O. Brizzi A, et al. Nat Med. 2022 Jul;28(7):1476-1485. doi: 10.1038/s41591-022-01807-1. Epub 2022 May 10. Nat Med. 2022. PMID: 35538260 Free PMC article.
Report 46: Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals.
Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete CA Jr, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro MC, Costa SF, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim DM, Miscouridou X, Mishra S, Monod M, Moreira FRR, Nelson B, Pereira RHM, Ranzani O, Schnekenberg RP, Semenova E, Sonnabend R, Souza RP, Xi X, Sabino EC, Faria NR, Bhatt S, Ratmann O. Brizzi A, et al. medRxiv [Preprint]. 2021 Nov 2:2021.11.01.21265731. doi: 10.1101/2021.11.01.21265731. medRxiv. 2021. Update in: Nat Med. 2022 Jul;28(7):1476-1485. doi: 10.1038/s41591-022-01807-1. PMID: 34751273 Free PMC article. Updated. Preprint.
Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status.
Fonseca PLC, Moreira FRR, de Souza RM, Guimarães NR, Carvalho NO, Adelino TER, Alves HJ, Alvim LB, Candido DS, Coelho HP, Costa AVB, Costa WC, de Carvalho AF, de Faria BWF, de Lima AB, de Oliveira ES, de Souza CSA, de Souza FG, Dias RC, Geddes VEV, Godinho IP, Gonçalves AL, Lourenço KL, Magalhães RDM, Malta FSV, Medeiros ELA, Mendes FS, Mendes PHBP, Mendonça CPTB, Menezes AL, Menezes D, Menezes MT, Miguita L, Moreira RG, Peixoto RB, Queiroz DC, Ribeiro AA, Ribeiro APB, Saliba JW, Sato HI, Silva JDP, Silva NP, Faria NR, Teixeira SMR, da Fonseca FG, Fernandes APSM, Zauli DAG, Januario JN, de Oliveira JS, Iani FCM, de Aguiar RS, de Souza RP. Fonseca PLC, et al. Virus Evol. 2022 Jul 27;8(2):veac064. doi: 10.1093/ve/veac064. eCollection 2022 Jul. Virus Evol. 2022. PMID: 35996592 Free PMC article.
Lessons from a Multilaboratorial Task Force for Diagnosis of a Fatal Toxoplasmosis Outbreak in Captive Primates in Brazil.
Schiffler FB, Pereira AHB, Moreira SB, Arruda IF, Moreira FRR, D'arc M, Claro IM, Pissinatti TA, Cavalcante LTF, Miranda TDS, Cosentino MAC, de Oliveira RC, Fernandes J, Assis MRDS, de Oliveira JG, da Silva TAC, Galliez RM, Faffe DS, de Jesus JG, Sobreira Bezerra da Silva M, Bezerra MF, Ferreira Junior ODC, Tanuri A, Castiñeiras TM, Aguiar RS, Faria NR, Almeida AP, Pissinatti A, Sabino EC, Amendoeira MRR, de Lemos ERS, Ubiali DG, Santos AFA. Schiffler FB, et al. Microorganisms. 2023 Nov 29;11(12):2888. doi: 10.3390/microorganisms11122888. Microorganisms. 2023. PMID: 38138032 Free PMC article.
Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022.
Claro IM, Romano CM, Candido DDS, Lima EL, Lindoso JAL, Ramundo MS, Moreira FRR, Barra LAC, Borges LMS, Medeiros LA, Tomishige MYS, Moutinho T, Silva AJDD, Rodrigues CCM, Azevedo LCF, Villas-Boas LS, Silva CAMD, Coletti TM, Manuli ER, O'Toole A, Quick J, Loman N, Rambaut A, Faria NR, Figueiredo-Mello C, Sabino EC. Claro IM, et al. Rev Inst Med Trop Sao Paulo. 2022 Jun 24;64:e48. doi: 10.1590/S1678-9946202264048. eCollection 2022. Rev Inst Med Trop Sao Paulo. 2022. PMID: 35749419 Free PMC article.