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.

Long Term Wastewater Based Epidemiology Of Sars-Cov-2 And Social Restrictions Applied In Porto Alegre, Southern Brazil

Wastewater-based epidemiology (WBE) may be successfully used to comprehensively monitor and determine the scale and dynamics of some infections in the community. We monitored severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in raw wastewater samples from Porto Alegre, Southern Brazil. The samples were collected and analyzed every week between May 2020 to May 2021. Meanwhile, different social restrictions were applied according to the number of hospitalized patients in the region. Weekly samples were obtained from two wastewater treatment plants (WWTP) (named Navegantes and Serraria). To determine the SARS-CoV-2 RNA titers in wastewater, we performed RT-qPCR analysis targeting the N gene (N1). The highest titer of SARS-CoV-2 RNA was observed between epidemiological weeks (EW) 33-37 (August), 42-43 (October), 45-46 (November), 49-51 (December) in 2020, and 1-3 (January), 7-13 (February to March) in 2021, with viral loads ranging from 1 x 106 ∼ 3 x 106 genomic copies/Liter. An increase in positive confirmed cases followed such high viral loads. Depending on the sampling method used, positive cases increased in 6∼7 days and 15 days after the rise of viral RNA titers in wastewater, with composite sampling methods showing a lower time lag and a higher resolution on the analyses. The results showed a direct relation between strict social restrictions and the loads of detected RNA reduction in wastewater, corroborating the number of confirmed cases. Differences in viral loads between different sampling points and methods were observed, as composite samples showed more stable results during the analyzed period. Besides, viral loads obtained from samples collected at Serraria WWTP were consistently higher than the ones obtained at Navegantes WWTP, indicating differences in local dynamics of SARS-CoV-2 spread in different regions of Porto Alegre. In conclusion, wastewater sampling to monitor SARS-CoV-2 is a robust tool to evaluate the viral loads contributing to hospitalized patients' data and confirmed cases. In addition, SARS-CoV-2 detection in sewage may inform and alert the government when the number of asymptomatic or non/tested patients is in evidence. Graphical [Image 1].

Long Term Wastewater Based Epidemiology Of Sars-Cov-2 And Social Restrictions Applied In Porto Alegre, Southern Brazil

Wastewater-based epidemiology (WBE) may be successfully used to comprehensively monitor and determine the scale and dynamics of some infections in the community. We monitored severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in raw wastewater samples from Porto Alegre, Southern Brazil. The samples were collected and analyzed every week between May 2020 to May 2021. Meanwhile, different social restrictions were applied according to the number of hospitalized patients in the region. Weekly samples were obtained from two wastewater treatment plants (WWTP) (named Navegantes and Serraria). To determine the SARS-CoV-2 RNA titers in wastewater, we performed RT-qPCR analysis targeting the N gene (N1). The highest titer of SARS-CoV-2 RNA was observed between epidemiological weeks (EW) 33-37 (August), 42-43 (October), 45-46 (November), 49-51 (December) in 2020, and 1-3 (January), 7-13 (February to March) in 2021, with viral loads ranging from 1 x 106 ∼ 3 x 106 genomic copies/Liter. An increase in positive confirmed cases followed such high viral loads. Depending on the sampling method used, positive cases increased in 6∼7 days and 15 days after the rise of viral RNA titers in wastewater, with composite sampling methods showing a lower time lag and a higher resolution on the analyses. The results showed a direct relation between strict social restrictions and the loads of detected RNA reduction in wastewater, corroborating the number of confirmed cases. Differences in viral loads between different sampling points and methods were observed, as composite samples showed more stable results during the analyzed period. Besides, viral loads obtained from samples collected at Serraria WWTP were consistently higher than the ones obtained at Navegantes WWTP, indicating differences in local dynamics of SARS-CoV-2 spread in different regions of Porto Alegre. In conclusion, wastewater sampling to monitor SARS-CoV-2 is a robust tool to evaluate the viral loads contributing to hospitalized patients' data and confirmed cases. In addition, SARS-CoV-2 detection in sewage may inform and alert the government when the number of asymptomatic or non/tested patients is in evidence.

Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil.

Tocantins is a state in the cross-section between the Central-West, North and Northeast regions of Brazilian territory; it is a gathering point for travelers and transportation from the whole country. In this study, 9493 genome sequences, including 241 local SARS-CoV-2 samples (collected from 21 December 2020, to 16 December 2021, and sequenced in the MinION platform) were analyzed with the following aims: (i) identify the relative prevalence of SARS-CoV-2 lineages in the state of Tocantins; (ii) analyze them phylogenetically against global SARS-CoV-2 sequences; and (iii) hypothesize the viral dispersal routes of the two most abundant lineages found in our study using phylogenetic and phylogeographic approaches. The performed analysis demonstrated that the majority of the strains sequenced during the period belong to the Gamma P.1.7 (32.4%) lineage, followed by Delta AY.99.2 (27.8%), with the first detection of VOC Omicron. As expected, there was mainly a dispersion of P.1.7 from the state of São Paulo to Tocantins, with evidence of secondary spreads from Tocantins to Goiás, Mato Grosso, Amapá, and Pará. Rio de Janeiro was found to be the source of AY.99.2 and from then, multiple cluster transmission was observed across Brazilian states, especially São Paulo, Paraiba, Federal District, and Tocantins. These data show the importance of trade routes as pathways for the transportation of the virus from Southeast to Northern Brazil.

Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil

Tocantins is a state in the cross-section between the Central-West, North and Northeast regions of Brazilian territory;it is a gathering point for travelers and transportation from the whole country. In this study, 9493 genome sequences, including 241 local SARS-CoV-2 samples (collected from 21 December 2020, to 16 December 2021, and sequenced in the MinION platform) were analyzed with the following aims: (i) identify the relative prevalence of SARS-CoV-2 lineages in the state of Tocantins;(ii) analyze them phylogenetically against global SARS-CoV-2 sequences;and (iii) hypothesize the viral dispersal routes of the two most abundant lineages found in our study using phylogenetic and phylogeographic approaches. The performed analysis demonstrated that the majority of the strains sequenced during the period belong to the Gamma P.1.7 (32.4%) lineage, followed by Delta AY.99.2 (27.8%), with the first detection of VOC Omicron. As expected, there was mainly a dispersion of P.1.7 from the state of São Paulo to Tocantins, with evidence of secondary spreads from Tocantins to Goiás, Mato Grosso, Amapá, and Pará. Rio de Janeiro was found to be the source of AY.99.2 and from then, multiple cluster transmission was observed across Brazilian states, especially São Paulo, Paraiba, Federal District, and Tocantins. These data show the importance of trade routes as pathways for the transportation of the virus from Southeast to Northern Brazil.

No Evidence of SARS-CoV-2 Infection in Neotropical Primates Sampled During COVID-19 Pandemic in Minas Gerais and Rio Grande do Sul, Brazil.

In 2019, a new coronavirus disease (COVID-19) was detected in China. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was capable to infect domestic and captive mammals like cats, tigers and minks. Due to genetic similarities, concern about the infection of non-human primates (NHPs) and the establishment of a sylvatic cycle has grown in the Americas. In this study, neotropical primates (NP) were sampled in different areas from Brazil to investigate whether they were infected by SARS-CoV-2. A total of 89 samples from 51 NP of four species were examined. No positive samples were detected via RT-qPCR, regardless of the NHP species, tissue or habitat tested. This work provides the first report on the lack of evidence of the circulation of SARS-CoV-2 in NP. The expansion of wild animals sampling is necessary to understand their role in the epidemiology of SARS-CoV-2 and other potentially zoonotic pathogens in natural environments shared by humans.

Validation of conventional PCR-like alternative to SARS-CoV-2 detection with target nucleocapsid protein gene in naso-oropharyngeal samples.

SARS-CoV-2 has spread worldwide and has become a global health problem. As a result, the demand for inputs for diagnostic tests rose dramatically, as did the cost. Countries with inadequate infrastructure experience difficulties in expanding their qPCR testing capacity. Therefore, the development of sensitive and specific alternative methods is essential. This study aimed to develop, standardize, optimize, and validate conventional RT-PCR targeting the N gene of SARS-CoV-2 in naso-oropharyngeal swab samples compared to qPCR. Using bioinformatics tools, specific primers were determined, with a product expected to be 519 bp. The reaction conditions were optimized using a commercial positive control, and the detection limit was determined to be 100 fragments. To validate conventional RT-PCR, we determined a representative sampling of 346 samples from patients with suspected infection whose diagnosis was made in parallel with qPCR. A sensitivity of 92.1% and specificity of 100% were verified, with an accuracy of 95.66% and correlation coefficient of 0.913. Under current Brazilian conditions, this method generates approximately 60% savings compared to qPCR costs. Conventional RT-PCR, validated herein, showed sufficient results for the detection of SARS-CoV-2 and can be used as an alternative for epidemiological studies and interspecies correlations.

High Rate of Mutational Events in SARS-CoV-2 Genomes across Brazilian Geographical Regions, February 2020 to June 2021.

Brazil was considered one of the emerging epicenters of the coronavirus pandemic in 2021, experiencing over 3000 daily deaths caused by the virus at the peak of the second wave. In total, the country had more than 20.8 million confirmed cases of COVID-19, including over 582,764 fatalities. A set of emerging variants arose in the country, some of them posing new challenges for COVID-19 control. The goal of this study was to describe mutational events across samples from Brazilian SARS-CoV-2 sequences publicly obtainable on Global Initiative on Sharing Avian Influenza Data-EpiCoV (GISAID-EpiCoV) platform and to generate indexes of new mutations by each genome. A total of 16,953 SARS-CoV-2 genomes were obtained, which were not proportionally representative of the five Brazilian geographical regions. A comparative sequence analysis was conducted to identify common mutations located at 42 positions of the genome (38 were in coding regions, whereas two were in 5' and two in 3' UTR). Moreover, 11 were synonymous variants, 27 were missense variants, and more than 44.4% were located in the spike gene. Across the total of single nucleotide variations (SNVs) identified, 32 were found in genomes obtained from all five Brazilian regions. While a high genomic diversity has been reported in Europe given the large number of sequenced genomes, Africa has demonstrated high potential for new variants. In South America, Brazil, and Chile, rates have been similar to those found in South Africa and India, providing enough "space" for new mutations to arise. Genomic surveillance is the central key to identifying the emerging variants of SARS-CoV-2 in Brazil and has shown that the country is one of the "hotspots" in the generation of new variants.

31st Brazilian Online Society for Virology (SBV) 2020 Annual Meeting.

The year 2020 was profoundly marked by the emergence and spread of SARS-CoV-2, causing COVID-19, which represents the greatest pandemic of the 21st century until now, and a major challenge for virologists in the scientific and medical communities. Increased numbers of SARS-CoV-2 infection all over the world imposed social and travel restrictions, including avoidance of face-to-face scientific meetings. Therefore, for the first time in history, the 2020 edition of the Brazilian Society of Virology (SBV) congress was totally online. Despite the challenge of the new format, the Brazilian society board and collaborators were successful in virtually congregating more than 921 attendees, which was the greatest SBV participant number ever reached. Seminal talks from prominent national and international researchers were presented every night, during a week, and included discussions about environmental, basic, animal, human, plant and invertebrate virology. A special roundtable debated exclusively new data and perspectives regarding COVID-19 by some of the greatest Brazilian virologists. Women scientists were very well represented in another special roundtable called "Young Women Inspiring Research", which was one of the most viewed and commented section during the meeting, given the extraordinary quality of the presented work. Finally, SBV offered the Helio Gelli Pereira award for one graduate and one undergraduate student, which has also been a fruitful collaboration between the society and Viruses journal. The annual SBV meeting has, therefore, reached its goals to inspire young scientists, stimulate high-quality scientific discussion and to encourage global collaboration between virologists.

Special Issue "Emerging Viruses 2020: Surveillance, Prevention, Evolution and Control".

This Special Issue of Viruses is a collection of the current knowledge on a broad range of emerging human, animal, and plant viral diseases [...].

Modeling transmission dynamics of severe acute respiratory syndrome coronavirus 2 in São Paulo, Brazil.

INTRODUCTION: Severe acute respiratory syndrome coronavirus 2 has been transmitted to more than 200 countries, with 92.5 million cases and 1,981,678 deaths. METHODS: This study applied a mathematical model to estimate the increase in the number of cases in São Paulo state, Brazil during four epidemic periods and the subsequent 300 days. We used different types of dynamic transmission models to measure the effects of social distancing interventions, based on local contact patterns. Specifically, we used a model that incorporated multiple transmission pathways and an environmental class that represented the pathogen concentration in the environmental reservoir and also considered the time that an individual may sustain a latent infection before becoming actively infectious. Thus, this model allowed us to show how the individual quarantine and active monitoring of contacts can influence the model parameters and change the rate of exposure of susceptible individuals to those who are infected. RESULTS: The estimated basic reproductive number, R o , was 3.59 (95% confidence interval [CI]: 3.48 - 3.72). The mathematical model data prediction coincided with the real data mainly when the social distancing measures were respected. However, a lack of social distancing measures caused a significant increase in the number of infected individuals. Thus, if social distancing measures are not respected, we estimated a difference of at least 100,000 cases over the next 300 days. CONCLUSIONS: Although the predictive capacity of this model was limited by the accuracy of the available data, our results showed that social distancing is currently the best non-pharmacological measure.