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" [...].

Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil.

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

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.

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.

Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

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.

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.

Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

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.

SARS-CoV-2 genomic monitoring in the São Paulo State unveils new sublineages of the AY.43 strain

Delta VOC is highly diverse and more than 120 sublineages have been identified in Pango lineages with the continuous description of emerging ones. Brazil is now one of the most vaccinated countries against SARS-CoV-2 in the world which can enhance the emergence of viral mutations related to improved viral fitness. In this study, we identified two novel sublineages of the AY.43 lineage which were classified as AY.43.1 and AY.43.2 as observed on the specific clustering on the obtained phylogenetic tree. The novel sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for AY.43.1 and ORF1ab:G1155C for AY.43.2. The majority of the analyzed sequences of both lineages were Brazilian, which shows that probably these two emerging sublineages have Brazilian origin. It is still unknown how these two sublineages are disseminated in São Paulo State and Brazil and their potential impact on the ongoing vaccination process. However, the performed study reinforces the importance of the SARS-CoV-2 genome monitoring for timely identification of emerging SARS-CoV-2 variants which can impact the ongoing SARS-CoV-2 vaccination and public health policies.

Genome-Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle.

Brazil is one of the largest beef producers and exporters in the world with the Nelore breed representing the vast majority of Brazilian cattle (Bos taurus indicus). Despite the great adaptability of the Nelore breed to tropical climate, meat tenderness (MT) remains to be improved. Several factors including genetic composition can influence MT. In this article, we report a genome-wide analysis of copy number variation (CNV) inferred from Illumina® High Density SNP-chip data for a Nelore population of 723 males. We detected >2,600 CNV regions (CNVRs) representing ≈6.5% of the genome. Comparing our results with previous studies revealed an overlap in ≈1400 CNVRs (>50%). A total of 1,155 CNVRs (43.6%) overlapped 2,750 genes. They were enriched for processes involving guanosine triphosphate (GTP), previously reported to influence skeletal muscle physiology and morphology. Nelore CNVRs also overlapped QTLs for MT reported in other breeds (8.9%, 236 CNVRs) and from a previous study with this population (4.1%, 109 CNVRs). Two CNVRs were also proximal to glutathione metabolism genes that were previously associated with MT. Genome-wide association study of CN state with estimated breeding values derived from meat shear force identified 6 regions, including a region on BTA3 that contains genes of the cAMP and cGMP pathway. Ten CNVRs that overlapped regions associated with MT were successfully validated by qPCR. Our results represent the first comprehensive CNV study in Bos taurus indicus cattle and identify regions in which copy number changes are potentially of importance for the MT phenotype.

Anurofauna da floresta de restinga do Parque Estadual da Ilha do Cardoso, Sudeste do Brasil: composição de espécies e uso de sítios reprodutivos / Anuran fauna of the restinga forest of the Parque Estadual da Ilha do Cardoso, Southeastern Brazil: species composition and breeding site utilization

O Parque Estadual da Ilha do Cardoso é uma área de grande importância para a conservação, pois abriga diferentes ecossistemas costeiros, como manguezais, dunas, restingas e mata atlântica de encosta, que, historicamente, estiveram sob forte pressão antrópica. A identificação duvidosa e a descoberta de novas espécies da anurofauna em ambientes costeiros, evidencia a escassez de estudos nessas regiões. Inventariamos a anurofauna da floresta de restinga do Parque Estadual da Ilha do Cardoso entre outubro de 2005 e outubro de 2007, por meio de 25 viagens mensais de dois dias de duração. Foram utilizados dois métodos: procura visual ativa em uma parcela permanente de 10 ha e procura visual e auditiva em nove sítios de reprodução. A anurofauna da área de estudo é composta por 17 espécies pertencentes às famílias Bufonidae (2 espécies), Craugastoridae (1), Hylidae (10), Leiuperidae (1), Leptodactylidae (2) e Microhylidae (1). A riqueza estimada foi de 17,77-17,96, o que mostra que nosso esforço amostral foi suficiente para registrar praticamente toda a anurofauna presente nessa formação de restinga. Essa riqueza pode ser considerada elevada quando comparada à de outras áreas de restinga, principalmente aquelas dotadas de vegetação menos estruturada. O predomínio da família Hylidae é característico de todas as localidades da região neotropical. Nenhuma espécie acha-se incluída nas listas de espécies ameaçadas de extinção do estado de São Paulo e do Brasil, mas Aparasphenodon bokermanni é considerada pouco conhecida ("Data Deficient") pela IUCN, e outras três espécies (Dendrophryniscus leucomystax, Haddadus binotatus e Itapotihyla langsdorffii) apresentam populações em declínio. Essas informações revelam a importância da floresta de restinga da Ilha do Cardoso para a manutenção de populações de anuros. Uma análise de agrupamento de 14 espécies que utilizaram nove sítios reprodutivos evidenciou três grupos, sendo o hidroperíodo o principal fator na determinação das similaridades. Conclui-se que a preservação de corpos d'água com diferentes fisionomias é essencial para a conservação de populações viáveis de anuros.

The Parque Estadual da Ilha do Cardoso is of great concern to conservation because it includes several coastal ecosystems, like mangroves, sand dunes, restingas, and Atlantic Rainforest, all of them under human pressure since Brazil discovery. The anuran fauna of Brazilian restingas remains poorly known; the discovery of new species and the dificulties to determine the anurans reflect the rarity of studies in these areas. We provide here a updated list of amphibians from the restinga Forest of the Parque Estadual da Ilha do Cardoso. Our inventory was conducted from October 2005 and October 2007, totaling 25 two-days trips. Two methods were applied: visual encounter survey in a 10 ha permanent plot and visual and acoustic survey in nine sites used by anurans for reproduction. The anuran fauna of the study site is composed by 17 species belonging to the families Bufonidae (2 species), Craugastoridae (1), Hylidae (10), Leiuperidae (1), Leptodactylidae (2), and Microhylidae (1). Estimated species richness was 17.77-17.96, which suggests our sampling effort was enough to adequately sample the anuran assemblage present in the area. This richness can be considered high when compared to the richness of other restinga areas, especially those with less structured vegetation. The dominance of the family Hylidae is common to all neotropical localities. None species is included in the lists of endangered species from the state of São Paulo and Brazil, but Aparasphenodon bokermanni is considered Data Deficient by IUCN, and other three species (Dendrophryniscus leucomystax, Haddadus binotatus and Itapotihyla langsdorffii) have decreasing populations. This information reveals the importance of the restinga forest of Ilha do Cardoso to the conservation of anuran populations. A cluster analysis of 14 species that used nine breeding sites resulted in three groups, and the hydroperiod can be considered the major factor influencing the similarities among species. We conclude that preserving water bodies with diferent physiognomies is essential for conserving viable anuran populations.

Anurofauna da Floresta Estacional Semidecidual da Estação Ecológica dos Caetetus, Sudeste do Brasil / Anuran fauna of the Semi-deciduous Forest of the Estação Ecológica dos Caetetus, Southeastern Brazil

A Floresta Estacional Semidecidual é considerada uma das formações florestais mais ameaçadas e suprimidas pela expansão agrícola do início do século passado, com sua cobertura vegetal reduzida a menos de 8 por cento da original. Estudos sobre taxocenoses de anfíbios anuros nessa formação florestal ainda são escassos, mesmo quando consideramos as poucas áreas de floresta primária que restaram. Apresentamos neste estudo os resultados de um levantamento de espécies de anfíbios anuros da Estação Ecológica dos Caetetus, uma unidade de conservação que abriga importante remanescente de Floresta Estacional Semidecidual na região Centro-oeste do estado de São Paulo, região considerada prioritária para conservação no estado. Foram registradas 34 espécies distribuídas em nove famílias, dentre as quais Hylidae e Leptodactylidae foram as que apresentaram as maiores riquezas, com 14 e oito espécies, respectivamente. A elevada riqueza de espécies da área, principalmente da família Hylidae, provavelmente está associada tanto à grande heterogeneidade ambiental dessa formação florestal como à sua localização em área de transição entre áreas de Cerrado e de Floresta Ombrófila. A alta riqueza de espécies, quando comparada à de outras áreas de mesma formação florestal, bem como a presença de representantes das famílias Centrolenidae, Craugastoridae e Hylodidae, que são dependentes de habitats florestais, atestam o bom estado de conservação e a importância regional desse remanescente florestal.

Semi-deciduous Forest is one of the most threatened and deforested vegetation types of Brazil due to its land conversion to agriculture in the beginning of the 20th Century; its distribution is now reduced to less than 8 percent of its original extent. Studies about anuran taxocenosis associated to these forests are scarce, even when we consider the remaining areas of pristine forest. We present herein results from an amphibian survey at the Estação Ecológica dos Caetetus, a conservation unit with a singular preserved Semi-deciduous Forest from the Middle-West region of the State of São Paulo, located inside the priority areas for conservation on São Paulo State. We provided here data on species richness, composition, geographical distribution, and natural history notes for each taxa found in the area. We recorded 34 anuran species belonging to nine families, of which Hylidae and Leptodactylidae are the two most speciose families, with 14 and eight species respectively. The high species richness in the area, mainly in the family Hylidae, can be explained by both the high environmental heterogeneity of this remnant and its geographic location between Cerrado savannas and Atlantic rain forest areas. Its high species richness when compared with other localities of the same vegetation type, as well as the presence of forest dependent species in the families Centrolenidae, Hylodidae and Craugastoridae, indicate both the good conservation status and the regional importance of this forest remnant.