Retrospective Insights of the COVID-19 Epidemic in the Major Latin American City, São Paulo, Southeastern Brazil.

São Paulo is the financial center of Brazil, with a population of over 12 million, that receives travelers from all over the world for business and tourism. It was the first city in Brazil to report a case of COVID-19 that rapidly spread across the city despite the implementation of the restriction measures. Despite many reports, much is still unknown regarding the genomic diversity and transmission dynamics of this virus in the city of São Paulo. Thus, in this study, we provide a retrospective overview of the COVID-19 epidemic in São Paulo City, Southeastern, Brazil, by generating a total of 9995 near-complete genome sequences from all the city's different macro-regions (North, West, Central, East, South, and Southeast). Our analysis revealed that multiple independent introduction events of different variants (mainly Gamma, Delta, and Omicron) occurred throughout time. Additionally, our estimates of viral movement within the different macro-regions further suggested that the East and the Southeast regions were the largest contributors to the Gamma and Delta viral exchanges to other regions. Meanwhile, the North region had a higher contribution to the dispersion of the Omicron variant. Together, our results reinforce the importance of increasing SARS-CoV-2 genomic monitoring within the city and the country to track the real-time evolution of the virus and to detect earlier any eventual emergency of new variants of concern that could undermine the fight against COVID-19 in Brazil and worldwide.

Correction: Lesbon et al. Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results. Viruses 2021, 13, 2474.

The authors hereby request the inclusion of two authors (Olivia Teixeira and Maria Cristina Nonato) in the recently published article in Viruses entitled "Nucleocapsid (N) gene mutations of SARS-CoV-2 can affect real-time RT-PCR diagnostic and impact false-negative results" [...].

ANÁLISE DA DISPERSÃO TEMPORAL E EPIDEMIOLÓGICA DAS VARIANTES DO SARS-COV-2 NO PERÍODO DE PRÉ-VACINAÇÃO EM MASSA NA CIDADE DE BOTUCATU-SP

Introdução Após a circulação das Variantes de Preocupação (VOC) do SARS-CoV-2, Alpha, Beta, Gamma, Delta e, a atualmente predominante, Ômicron, a ampla cobertura vacinal refletiu na drástica redução nos números de óbitos por COVID-19. Em maio de 2021, o município de Botucatu-SP foi palco de uma pesquisa que avaliou a efetividade da Vacina COVID-19 Recombinante/Fiocruz® contra variantes do SARS-CoV-2, possibilitando imunização de mais de 60 mil pessoas em um único dia. Objetivo Avaliar a dispersão temporal e epidemiológica das variantes do SARS-CoV-2 antes da vacinação massiva que ocorreu em Botucatu, além de relacioná-las às características clínicas da doença. Método Foram selecionadas 400 amostras SARS-CoV-2 positivas, referentes as 4 Semanas Epidemiológicas (SE 16, 17, 18 e 19 de 2021 – sendo 100 amostras por SE) que antecederam a campanha da vacinação em massa. O Sequenciamento de Nova Geração foi utilizado para produzir as sequências e determinar as variantes. Informações clínicas foram extraídas dos relatórios de notificação de casos suspeitos de COVID-19 (E-Sus) e de internação por Síndrome Respiratória Aguda Grave (Sivep-Gripe). Resultados Entre todas as amostras positivas incluídas, 86,8% eram de pessoas não vacinadas. Foram geradas e analisadas 371 sequências de alta qualidade. Dessas sequências, 98,65% foram da VOC Gamma e 1,35% da VOC Alpha. Dentro do clado de Gamma, a variante P.1 foi mais frequente (55%) seguida pela sua sublinhagem P.1.14 (42,3%). Quanto a distribuição das VOCs entre diferentes faixas etárias e sexo, a P.1 foi mais incidente do que a P.1.14 nas de 21-30 anos (p < 0,001) e 51-60 (p = 0,047), e em mulheres (p = 0,002). A incidência desta VOC também foi maior para casos leves da doença (p < 0,001). A sublinhagem P.1.14 foi mais incidente do que P.1 apenas em pessoas com idade entre 81-90 anos (p = 0,034). As amostras com menores valores de CT foram mais associadas aos pacientes sintomáticos (p = 0,005). Não houve correlação entre as variantes e a presença de comorbidades nos infectados, tampouco entre elas e os desfechos clínicos internação ou óbito. Conclusão A alta predominância de P.1 e P.1.14 em um cenário pré-vacinação em massa pode nos fornecer insights sobre a evolução e epidemiologia molecular do SARS-CoV-2 e suas VOCs emergentes. Dessa forma ressaltamos a importância da vigilância genômica do SARS-CoV-2, que pode ajudar a subsidiar as tomadas de decisões dos setores públicos e manejo da COVID-19.

The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela.

Our effort in SARS-CoV-2 genomic surveillance in Brazil has detected the Alpha Variant of Concern with a predominance higher than 75% in the population of Ilhabela island (São Paulo State) at a time when the Gamma VOC was already predominating the mainland raised concerns for closer surveillance on this island. Therefore, we intensified the surveillance for 24 weeks by generating data from 34% of local positive cases. Our data show that the patterns of VOC predominance dynamics and infection rates were in general distinct from the mainland. We report here the first known case of Alpha predominance in a Brazilian population, a delay greater than 3 months for the Gamma to dominate the previous variants compared to the mainland, and a faster dispersion rate of Gamma and Delta VOCs compared to the mainland. Phylogenetic analysis revealed the SARS-CoV-2 transmission dynamics in Ilhabela were characterized by multiple independent introduction events of Gamma and Delta, with a few events of Alpha introduction, two of them followed by community transmission. This study evidenced the peculiar behavior of SARS-CoV-2 variants in an isolated population and brought to light the importance of specific programs for SARS-CoV-2 genomic surveillance in isolated populations.

SARS-COV-2 genomic monitoring in the state of São Paulo unveils two emerging AY.43 sublineages.

Delta VOC is highly diverse with more than 120 sublineages already described as of November 30, 2021. In this study, through active monitoring of circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants in the state of São Paulo, southeast Brazil, we identified two emerging sublineages from the ancestral AY.43 strain which were classified as AY.43.1 and AY.43.2. These sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for the AY.43.1 and ORF1ab:G1155C for the AY.43.2 and our analysis reveals that they might have a likely-Brazilian origin. Much is still unknown regarding their dissemination in the state of São Paulo and Brazil as well as their potential impact on the ongoing vaccination process. However, the results obtained in this study reinforce the importance of genomic surveillance activity for timely identification of emerging SARS-CoV-2 variants which can impact the ongoing SARS-CoV-2 vaccination and public health policies.

Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results.

The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection but with RDRP (RNA-dependent RNA polymerase) and E (Envelope) genes detection, and observed a set of three different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution of GGG to AAC (28881-28883) and a frameshift mutation caused by deletion (Del28877-28878). The last one cause a deletion of six AAs (amino acids) located in the central intrinsic disorder region at protein level. We also found this mutation in 99 of the 14,346 sequenced samples by the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants, demonstrating the circulation of the mutation in Sao Paulo, Brazil. Continuous monitoring and characterization of mutations affecting the annealing sites of primers and probes by genomic surveillance programs are necessary to maintain the effectiveness of the diagnosis of COVID-19.

Genomic monitoring of the SARS-CoV-2 B1.1.7 (WHO VOC Alpha) in the Sao Paulo state, Brazil.

The SARS-CoV-2 alpha VOC (also known as lineage B.1.1.7) initially described in the autumn, 2020 in UK, rapidly became the dominant lineage across much of Europe. Despite multiple studies reporting molecular evidence suggestive of its circulation in Brazil, much is still unknown about its genomic diversity in the state of São Paulo, the main Brazilian economic and transportation hub. To get more insight regarding its transmission dynamics into the State we performed phylogenetic analysis on all alpha VOC strains obtained between February and August 2021 from the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants. The performed phylogenetic analysis showed that most of the alpha VOC genomes were interspersed with viral strains sampled from different Brazilian states and other countries suggesting that multiple independent Alpha VOC introductions from Brazil and overseas have occurred in the São Paulo State over time. Nevertheless, large monophyletic clusters were also observed especially from the Central-West part of the São Paulo State (the city of Bauru) and the metropolitan region of the São Paulo city. Our results highlight the Alpha VOC molecular epidemiology in the São Paulo state and reinforce the need for continued genomic surveillance strategies for the real-time monitoring of potential emerging SARS-CoV-2 variants during the ever-growing vaccination process.