Investigação molecular e temporal da circulação do SARS-CoV-2 no município de São José do Rio Preto (SP)

Abstract

Introduction: SARS-CoV-2 is one of the seven coronaviruses that can cause human infection. The virus was detected for the first time in Wuhan — China at the end of 2019 and months later spread worldwide, causing the COVID-19 pandemic. The disease usually causes mild symptoms. The presence of comorbidities and advanced age are risk factors for severe COVID-19. Brazil was strongly affected by the pandemic. São José do Rio Preto, a medium-sized city in the Northwest region of São Paulo, was the third city in the State in number of COVID-19 cases and deaths. The municipality harbors Hospital de Base, which is a reference health center in São Paulo State. Although much is known about the course of the pandemic from the emergence of the VOIs and VOCSs, very little information is available about the SARS-CoV-2 spread and evolution in early 2020 in Brazil. Objectives: This study aimed to investigate the dynamic circulation of SARSCoV- 2 in São José do Rio Preto, an important city in the context of the pandemic in São Paulo State, from March to November 2020 through genomic surveillance. Materials and Methods: We used nasopharyngeal COVID-19 positive samples collected from São José do Rio Preto residents from March to November 2020. RNA was extracted and then RT-gPCR was performed to determine the cycle threshold (Ct). Samples were selected for library preparation and sequencing based on the Ct values. The generated genomes were assembled and those with 90% above coverage were used for phylogenetic and phylogeography analyses. Besides, maps were created after geoprocessing analysis. Results: Overall, the present study generated 627 SARS-CoV-2 whole genomes. The lineages B.1.1.28, B.1.1.33, B.1.1, N.9, Zeta, B.1, B.1.212, B.1.499, N.3, and P.7 were circulating in São José do Rio Preto between March and November 2020. B.1.1.28 and B.1.1.33 were the first lincages introduced and the most prevalent ones in the city during the study period. Zeta and N.9 were detected in March and April, respectively. The lineages B.1.1.28, B.1.1.33, and Zeta disseminated across Brazil in different periods from the southeast region. Exportation events of B.1.1.28 and B.1.1.33 occurred mostly from São José do Rio Preto to the southeast region, while Zeta was exported essentially from São José do Rio Preto to the northeast region. Conclusions: This study generated most of the SARS-CoV-2 genomes from São José do Rio Preto from 2020. A total of 10 different lineages were detected in the municipality from March to November 2020. The data obtained showed Zeta originated before July 2020, as proposed in scientific literature, since the VOTI's first detection was in March 2020. São José do Rio Preto contributed to B.1.1.28, B.1.1.33, and Zeta spread across Brazil.