Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022

Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation.

Viral metagenomics; Monkeypox virus; West African clade; Genomic surveillance; Brazil

Authorship

Ingra Morales Claro

Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, BrazilUniversidade de São PauloBrazilSão Paulo, São Paulo, BrazilUniversidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil

Imperial College London, MRC Centre for Global Infectious Disease Analysis, London, United KingdomImperial College LondonUnited KingdomLondon, United KingdomImperial College London, MRC Centre for Global Infectious Disease Analysis, London, United Kingdom

http://orcid.org/0000-0001-8637-2910

Camila Malta Romano

http://orcid.org/0000-0003-4550-1987

Darlan da Silva Candido

University of Oxford, Department of Zoology, Oxford, United KingdomUniversity of OxfordUnited KingdomOxford, United KingdomUniversity of Oxford, Department of Zoology, Oxford, United Kingdom

Evelyn Lepka de Lima

Instituto de Infectologia Emílio Ribas, São Paulo, São Paulo, BrazilInstituto de Infectologia Emílio RibasBrazilSão Paulo, São Paulo, BrazilInstituto de Infectologia Emílio Ribas, São Paulo, São Paulo, Brazil

José Angelo Lauletta Lindoso

Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, BrazilUniversidade de São PauloBrazilSão Paulo, São Paulo, BrazilUniversidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil

http://orcid.org/0000-0002-4405-4401

Mariana Severo Ramundo

Filipe Romero Rebello Moreira

Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Rio de Janeiro, Rio de Janeiro, BrazilUniversidade Federal do Rio de JaneiroBrazilRio de Janeiro, Rio de Janeiro, BrazilUniversidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Genética, Rio de Janeiro, Rio de Janeiro, Brazil

Luiz Alberto Costa Barra

Luciana Marques Sansão Borges

Lucas Alberto Medeiros

Marcia Y. S. Tomishige

Tomas Moutinho

http://orcid.org/0000-0002-0375-1366

Anderson José Dias da Silva

Camila Cristina Martini Rodrigues

Luiz Cesar Fernandes de Azevedo

Lucy Santos Villas-Boas

Camila Alves Maia da Silva

http://orcid.org/0000-0002-4298-6782

Thaís Moura Coletti

Erika R. Manuli

http://orcid.org/0000-0003-2376-8488

Aine O’Toole

University of Edinburgh, Institute of Ecology and Evolution, Edinburgh, United KingdomUniversity of EdinburghUnited KingdomEdinburgh, United KingdomUniversity of Edinburgh, Institute of Ecology and Evolution, Edinburgh, United Kingdom

Joshua Quick

University of Birmingham, School of Biosciences, Birmingham, United KingdomUniversity of BirminghamUnited KingdomBirmingham, United KingdomUniversity of Birmingham, School of Biosciences, Birmingham, United Kingdom

Nicholas Loman

Andrew Rambaut

Nuno R. Faria

University of Oxford, Department of Zoology, Oxford, United KingdomUniversity of OxfordUnited KingdomOxford, United KingdomUniversity of Oxford, Department of Zoology, Oxford, United Kingdom

Claudia Figueiredo-Mello

Ester Cerdeira Sabino

http://orcid.org/0000-0003-2623-5126

Correspondence to: Ester Cerdeira Sabino Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, 470, Cerqueira César, CEP 05403 000, São Paulo, SP, Brazil Tel: +55 11 99641 6284 E-mail: sabinoec@usp.br.

Nuno R. Faria Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, 470, Cerqueira César, CEP 05403 000, São Paulo, SP, Brazil Tel: +44 7546 407733 E-mail: nfaria@ic.ac.uk

AUTHORS’ CONTRIBUTIONS

Conceptualization: IMC, CMR, DSC, MSR, FRRM, NRF, and ECS; data curation:, IMC, CRM, DSC, FRRM, AOT, NL, AR, NRF, CFM, and ECS; formal analysis: IMC, CMR, DSC, FRRM, AOT, NL, AR, and NRF; funding acquisition: AR, NL, NRF, and ECS; investigation: IMC, CMR, DSC, ELL, JALL, MSR, FRRM, LACB, LMSB, LAM, MYST, TM, AJDS, CCMR, LCFA, LSVB, CAMS, TMC, ERM, AOT, JQ, NL, AR, NRF, CFM, and ECS; methodology: IMC, CMR, DSC, MSR, FRRM, TM, LSVB, CAMS, TMC, AOT, JQ, NL, AR, and NRF; resources: AR, NL, NRF, CFM, and ECS; validation: IMC, JQ, NL, AR, and NRF; writing (original draft): IMC, CMR, DSC, MSR, FRRM, and NRF; writing (review and editing): IMC, CMR, DSC, JALL, MSR, FRRM, NL, AR, NRF, CFM, and ECS.

SCIMAGO INSTITUTIONS RANKINGS

University of Oxford, Department of Zoology, Oxford, United KingdomUniversity of OxfordUnited KingdomOxford, United KingdomUniversity of Oxford, Department of Zoology, Oxford, United Kingdom

Figures

Figures (1)

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Figure 1
Maximum likelihood phylogeny with 103 whole genome MPXV sequences, including 102 available in NCBI GenBank up to June 9, 2022 (see Supplementary Table S1 for the Accession Numbers used in this study). Highlighted genomes (yellow tips), including the SP01 described in this study (red tip), belong to the newly proposed B.1 lineage³3. Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, et al. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. Virological.org. [cited 2022 Jun 20]. Available from: https://virological.org/t/urgent-need-for-a-non-discriminatory-and-non-stigmatizing-nomenclature-for-monkeypox-virus/853
https://virological.org/t/urgent-need-fo... . An interactive visualization of the phylogeny presented here can be found at Argimón et al.¹⁷17. Argimón S, Abudahab K, Goater RJ, Fedosejev A, Bhai J, Glasner C, et al. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom. 2016;2:e000093.

Figure 1 Maximum likelihood phylogeny with 103 whole genome MPXV sequences, including 102 available in NCBI GenBank up to June 9, 2022 (see Supplementary Table S1 for the Accession Numbers used in this study). Highlighted genomes (yellow tips), including the SP01 described in this study (red tip), belong to the newly proposed B.1 lineage³3. Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, et al. Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. Virological.org. [cited 2022 Jun 20]. Available from: https://virological.org/t/urgent-need-for-a-non-discriminatory-and-non-stigmatizing-nomenclature-for-monkeypox-virus/853
https://virological.org/t/urgent-need-fo... . An interactive visualization of the phylogeny presented here can be found at Argimón et al.¹⁷17. Argimón S, Abudahab K, Goater RJ, Fedosejev A, Bhai J, Glasner C, et al. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom. 2016;2:e000093.

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Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022

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[1] Correspondence to: Ester Cerdeira Sabino Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, 470, Cerqueira César, CEP 05403 000, São Paulo, SP, Brazil Tel: +55 11 99641 6284 E-mail: sabinoec@usp.br.