The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub.

Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation.

Early introduction, dispersal and evolution of Delta SARS-CoV-2 in Southern Brazil, late predominance of AY.99.2 and AY.101 related lineages.

The emergence of Variants of Concern (VOC) presenting an unusual number of new mutations is one of the most remarkable features of SARS-CoV-2. The Delta variant, since its appearance, replaced the VOC Gamma, which was responsible for the major COVID-19 wave in Brazil. In this study, we performed a Delta whole-genome sequencing of 183 samples as part of a major genomic surveillance study performed since the beginning of the pandemic. Here, we showed an emergence, widespread dispersion and consolidation of the Delta variant in Rio Grande do Sul State, completely replacing the Gamma variant in a four to five months period. Performing the phylogenetic and phylodynamic analysis, the majority of the sequences generated herein were classified as AY.99.2, AY.99.2-like and AY.101. AY.99.2 Delta-related lineage has been widely reported in Brazil and in the Americas as well. Altogether, our findings provided a mutational profile of the sequences and presented high substitutions per site in the root-to-tip phylogenetic tree, corroborating studies that show the high mutational rate of SARS-CoV-2 over time.

[Social distancing as protection factor against COVID-19 in a non-metropolitan area in the State of Rio Grande do Sul, BrazilLas medidas de distanciamiento social como factor de protección contra la COVID-19 en el interior de Rio Grande do Sul, Brasil]. / Medidas de distanciamento social como fator de proteção contra a COVID-19 no interior do Rio Grande do Sul, Brasil.

OBJECTIVE: To estimate the SARS-CoV-2 seroprevalence in a non-metropolitan area (Vale do Rio Pardo) in the state of Rio Grande do Sul, Brazil, and determine the association between seroprevalence and adherence to social distancing measures. METHOD: For the present population-based, cross-sectional study, data were collected in four stages from August to October 2020. SARS-CoV-2 seroprevalence was assessed using an IgG/IgM rapid test. Demographic, socioeconomic, clinical, and behavioral data were also collected, with administration of a three-question survey to determine adherence to social distancing measures with a focus on the level of social distancing practiced by participants, their routine activities, and circulation of people in the home. The association between sociodemographic data and social distancing was assessed using the chi-square test for linear trends in proportions, and the association between social distancing and seroprevalence was assessed using Poisson regression (95% confidence interval [95%CI]; P< 0.05). RESULTS: Of 4 252 tested and interviewed participants, 11.8% (95%CI: 10.8; 12.8) did not adhere to social distancing measures. The prevalence of a positive rapid test was 4.7% in participants who did not practice social distancing and 1.9% in participants who adhered to social distancing measures (P< 0.05). The variables male sex, age 20 to 59 years, having completed high school, monthly family income ranging from R$ 3 136.00 to R$ 6 270.00, and living in rural areas were associated with non-adherence to social distancing (P< 0.05). Adherence to all social distancing measures provided protection against SARS-CoV-2 infection (prevalence ratio: 0.37; 95%CI: 0.19; 0.73). CONCLUSIONS: The results indicate a reduction in seroprevalence with the adherence to social distancing measures.

OBJETIVO: Investigar la seroprevalencia del SARS-CoV-2 en la zona del Vale do Rio Pardo (Rio Grande do Sul, Brasil), y analizar la relación entre la seroprevalencia y el cumplimiento de las medidas de distanciamiento social por parte de la población. MÉTODO: Este estudio transversal basado en la población comprendió cuatro etapas de recopilación domiciliaria de datos entre agosto y octubre del 2020. La seroprevalencia se evaluó con la prueba rápida de anticuerpos IgM e IgG. Además, se recopilaron datos demográficos, socioeconómicos, clínicos y comportamentales por medio de un cuestionario de tres preguntas sobre el cumplimiento de las medidas de distanciamiento social, centrado en el grado de distanciamiento social que la persona entrevistada lograba tener, la rutina de las actividades de la persona entrevistada y la circulación de personas en el hogar. La relación entre los datos sociodemográficos y la práctica de distanciamiento social se evaluó con la prueba del ji cuadrado para determinar la tendencia lineal y la heterogeneidad de las proporciones, y la relación entre el distanciamiento social y la seroprevalencia se evaluó con el modelo de regresión de Poisson (intervalo de confianza de 95% [IC95%]; P< 0,05). RESULTADOS: De las 4 252 personas que se entrevistaron y a las que se les realizó la prueba, 11,8% (IC95%: 10,8; 12,8) no cumplían el distanciamiento social. La prevalencia de la realización de la prueba rápida con reactivo fue de 4,7% entre quienes no cumplían el distanciamiento social y de 1,9% entre quienes cumplían con esa medida (P< 0,05). Las variables relacionadas con el sexo masculino, el grupo etario de 20 a 59 años, la escolaridad de nivel medio, los ingresos familiares mensuales de R$ 3 136,00 a R$ 6 270,00 y la residencia en zonas urbanas guardaron relación con el incumplimiento del distanciamiento social (P< 0,05). El cumplimiento con todas las medidas de distanciamiento social fue un factor de protección contra la infección por SARS-CoV-2 (razón de prevalencia: 0,37; IC95%: 0,19; 0,73). CONCLUSIONES: Los resultados indican una reducción de la seroprevalencia a causa de las medidas de distanciamiento social.

Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation.

Recently, the highest wave of SARS-CoV-2 epidemic occurred since the beginning of the pandemic in Brazil was registered in Rio Grande do Sul (RS) State, Southern Brazil, considering the number of cases, deaths and hospitalization per day caused by COVID-19. In this study we described which lineages were circulating in the first quarter of 2021 in Southern Brazil to better understand the viral factors involved in the health crisis caused by SARS-CoV-2 in the region, searching also for possible additional SARS-CoV-2 sequence mutations. A total of 70 positive SARS-CoV-2 samples collected between January 28th, 2021 until April 23rd, 2021, were selected to sequencing. Whole genome sequencing of 70 SARS-CoV-2 samples showed a predominance of Gamma lineage (67%, 47/70), followed by P.2 lineage (27%, 19/70) and B.1.1.28 (6%, 4/70). Two Gamma lineage consensus sequences presented a new S:D614A mutation. Newly mutations could be emerging due the quick SARS-CoV-2 spreading. Thus, the greater understanding about immune protection and variants vigilance is essential to the better management of the health SARS-CoV-2 crisis.