Dynamic clade transitions and the influence of vaccine rollout on the spatiotemporal circulation of SARS-CoV-2 variants in São Paulo, Brazil

Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.

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.

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.

Anuran fauna of the Parque Estadual Carlos Botelho - Núcleo Sete Barras, southeastern Brazil: species composition, use of breeding sites, and seasonal patterns of breeding activity

Abstract: The goal of this work was to study the species composition, the use of breeding sites, and the seasonal patterns of breeding activity of the anuran fauna from Parque Estadual Carlos Botelho - Núcleo Sete Barras, state of São Paulo, southeastern Brazil. Fieldwork was carried out from September 2005 to October 2007 through two main methods: active visual search inside a 10 ha- permanent plot and aural and visual search in seven previously selected aquatic breeding habitats. Species richness was related to the sampling effort by means of species accumulation curve and through non-parametric estimators. Thirty-three species distributed in 12 families were recorded, from which 69% are endemic to the Atlantic Forest. Trachycephalus mesophaeus represents a new record for the park. Cycloramphus lutzorum is included as Data Deficient in the IUCN list. The species accumulation curve did not stabilize, showing some tendency to rise. The use of breeding sites by 20 species was compared using cluster analysis, which revealed two major groups: the first with five species (two habitat generalists and three stream specialists) and the second composed by the other species (with different reproductive modes associated with flooded environments). The breeding period of most species was associated to the rainy season (October to February), and only Scinax hayii showed continuous breeding activity during the entire period of study.

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

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.

Anurofauna da Floresta Estacional Semidecidual da Estação Ecológica dos Caetetus, Sudeste do Brasil

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% 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.