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

Author(s):Show less -

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]

Affiliation

^[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

• Document type: Journal article
• Source: INFECTION GENETICS AND EVOLUTION; v. 93, SEP 2021.
• Web of Science Citations: 0

Abstract

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)

• FAPESP's process: 13/08135-2 - CTC - Center for Cell-Based Therapy
• Grantee: Dimas Tadeu Covas
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• FAPESP's process: 17/26950-6 - RED BLOOD CELL ALLOIMMUNIZATION IN SICKLE CELL DISEASE: IDENTIFICATION OF RH VARIANTS AND IMMUNE MARKERS
• Grantee: Evandra Strazza Rodrigues Sandoval
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 18/15826-5 - Evaluation of the impact of emerging and reemerging viruses in the field of hemotherapy and stem-cell transplantation by multiple-research approach
• Grantee: Svetoslav Nanev Slavov
• Support Opportunities: Scholarships in Brazil - Young Researchers