Molecular surveillance of the on-going SARS-COV-2 epidemic in Ribeirao Preto City, Brazil

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Slavov, Svetoslav Nanev ^[1] ; Giovanetti, Marta ^{[2, 3]} ; Bezerra, Rafael dos Santos ^[1] ; Fonseca, Vagner ^{[2, 4]} ; Santos, Elaine Vieira ^[1] ; Rodrigues, Evandra Strazza ^[1] ; Adelino, Talita ^{[2, 5]} ; Xavier, Joilson ^[2] ; Borges, Josiane Serrano ^[1] ; Evaristo, Mariane ^[1] ; Lima, Mauricio Teixeira ^[2] ; Pereira, Glauco de Carvalho ^[5] ; Yamamoto, Aparecida Yulie ^[6] ; Cle, Diego Villa ^[6] ; Calado, Rodrigo Tocantins ^{[1, 6]} ; Covas, Dimas Tadeu ^{[1, 6]} ; Alcantara, Luiz Carlos Junior ^{[2, 3]} ; Kashima, Simone ^[1]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Fac Med Ribeirao Preto, Blood Ctr Ribeirao Preto, Sao Paulo - Brazil

^[2] Univ Fed Minas Gerais, Lab Genet Celular & Mol, Belo Horizonte, MG - Brazil

^[3] Fundacao Oswaldo Cruz, Lab Flavivirus, Inst Oswaldo Cruz, Rio De Janeiro - Brazil

^[4] Univ KwaZulu Natal, Coll Hlth Sci, KwaZulu Natal Res Innovat & Sequencing Platform K, ZA-4001 Durban - South Africa

^[5] Fdn Ezequiel Dias, Lab Cent Saude Publ, Belo Horizonte, MG - Brazil

^[6] Univ Sao Paulo, Ribeirao Preto Med Sch, Dept Med Imaging Hematol & Oncol, Sao Paulo - Brazil

• Tipo de documento: Artigo Científico
• Fonte: INFECTION GENETICS AND EVOLUTION; v. 93, SEP 2021.
• Citações Web of Science: 0

Resumo

The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of an unprecedented worldwide pandemic. Brazil demonstrates one of the highest numbers of confirmed SARS-CoV-2 cases, and Sa similar to o Paulo State is the epicenter of the pandemics in the country. Nevertheless, little is known about the SARS-CoV-2 circulation in other cities in the State than Sa similar to o Paulo city. The objective of this study was to analyze phylogenetically SARS-CoV-2 strains circulating in city of Ribeira similar to o Preto at the beginning of the pandemic and during the actual second wave. Twenty-nine nasopharyngeal SARS-CoV-2 RNA positive samples were sequenced by nanopore technology (18 obtained at the initial period of the pandemic and 11 during the second wave) and analyzed them phylogenetically. The performed analysis demonstrated that the majority of the strains obtained in the initial period of the pandemic in Ribeira similar to o Preto belonged mainly to the B1.1.33 lineage (61.1%), but B.1.1 (27.8%) and B.1.1.28 (11.1%) lineages were also identified. In contrast, the second wave strains were composed exclusively by the Brazilian variant of concern (VOC) P.1 (91%) and P.2 (9%) lineages. The obtained phylogenetic results were suggestive of successive SARS-CoV-2 lineage substitution in this Brazilian region by the P.1 VOC. The performed study examines the SARS-CoV-2 genotypes in Ribeira similar to o Preto city via genomic surveillance data. The obtained findings can contribute for continuous long-term genomic surveillance of SARS-CoV-2 due to the accelerated dynamics of viral lineage substitution, predict further waves and examine lineage behavior during SARS-CoV-2 vaccination. (AU)

• Processo FAPESP: 13/08135-2 - CTC - Centro de Terapia Celular
• Beneficiário: Dimas Tadeu Covas
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs
• Processo FAPESP: 17/26950-6 - Aloimunização eritrocitária na doença falciforme: identificação de variantes do sistema rh e de marcadores imunológicos
• Beneficiário: Evandra Strazza Rodrigues Sandoval
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 18/15826-5 - Avaliação do impacto de vírus emergentes e re-emergentes em hemoterapia e transplante de células-tronco por meio de técnicas moleculares avançadas
• Beneficiário: Svetoslav Nanev Slavov
• Modalidade de apoio: Bolsas no Brasil - Jovens Pesquisadores