Lying in Wait: The Resurgence of Dengue Virus After the Zika Epidemic in Brazil

After the Zika virus (ZIKV) epidemic in the Americas in 2016, both Zika and dengue incidence declined to record lows in many countries in 2017-2018, but in 2019 dengue resurged in Brazil, causing ~2.1 million cases. In this study we use epidemiological, climatological and genomic data to investigate dengue dynamics in recent years in Brazil. First, we estimate dengue virus force of infection (FOI) and model mosquito-borne transmission suitability since the early 2000s. Our estimates reveal that DENV transmission was low in 2017-2018, despite conditions being suitable for viral spread. Our study also shows a marked decline in dengue susceptibility between 2002 and 2019, which could explain the synchronous decline of dengue in the country, partially as a result of protective immunity from prior ZIKV and/or DENV infections. Furthermore, we performed phylogeographic analyses using 69 newly sequenced genomes of dengue virus serotype 1 and 2 from Brazil, and found that the outbreaks in 2018-2019 were caused by local DENV lineages that persisted for 5-10 years, circulating cryptically before and after the Zika epidemic. We hypothesize that DENV lineages may circulate at low transmission levels for many years, until local conditions are suitable for higher transmission, when they cause major outbreaks

ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection

The COVID-19 pandemic is driven by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) that emerged in 2019 and quickly spread worldwide. Genomic surveillance has become the gold standard methodology used to monitor and study this fast-spreading virus and its constantly emerging lineages. The current deluge of SARS-CoV-2 genomic data generated worldwide has put additional pressure on the urgent need for streamlined bioinformatics workflows. Here, we describe a workflow developed by our group to process and analyze large-scale SARS-CoV-2 Illumina amplicon sequencing data. This workflow automates all steps of SARS-CoV-2 reference-based genomic analysis: data processing, genome assembly, PANGO lineage assignment, mutation analysis and the screening of intrahost variants. The pipeline is capable of processing a batch of around 100 samples in less than half an hour on a personal laptop or in less than five minutes on a server with 50 threads. The workflow presented here is available through Docker or Singularity images, allowing for implementation on laptops for small-scale analyses or on high processing capacity servers or clusters. Moreover, the low requirements for memory and CPU cores and the standardized results provided by ViralFlow highlight it as a versatile tool for SARS-CoV-2 genomic analysis

Ancient origin of Jingchuvirales derived glycoproteins integrated in arthropod genomes

Suplementary material of the linked paper.</p

RPGBIO DROGADIÇÃO: o jogo Role Playing Game (RPG) como prática no processo de ensino e aprendizagem

Este artigo tem por objetivo apresentar os resultados da elaboração e aplicação do jogo RPGBIO drogadição em instituições de ensino. Esse jogo é parte de um projeto desenvolvido para implementar uma prática educativa, com a finalidade de problematizar e discutir o tema drogadição nas instituições de ensino. Esse jogo tem como modelo as regras do Role Playing Game (RPG), onde cada jogador interpreta um personagem com as características que desejar, podendo interagir livremente com outros personagens, professores e estudantes, contemplando assim, a metodologia dialética. O material do jogo foi elaborado, adaptado e confeccionado por acadêmicos e docentes do curso de Licenciatura em Biologia da UNIPAMPA e do IFFar,RS e,  aplicado em quatro turmas de Licenciatura em Biologia e em dez turmas do Ensino Médio, resultando num ambiente de reflexão e questionamento. Além disso, verificou-se uma melhora na aprendizagem desta temática demonstrada pelo interesse e participação nas discussões, após o jogo. O referencial teórico e metodológico que embasa a proposta parte de Freire (1992, 1996, 2011) e Sartori (2013). O jogo se configura em uma proposta de ensino que alia conteúdos de Biologia a temas de cunho social, desafiando educadores e educandos a refletirem suas ações, frente às questões inquietantes do mundo

Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil

Fundação de Amparo à Pesquisa do Estado do Amazonas (PCTI-EmergeSaude/AM call 005/2020 and Rede Genômica de Vigilância em Saúde-REGESAM); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (grant 402457/2020–0); CNPq/Ministério da Ciência, Tecnologia, Inovação e Comunicação/Ministério da Saúde (MS/FNDCT/ SCTIE/Decit) (grant 403276/2020-9); Departamento da Ciência e Tecnologia (DECIT), Ministério da Saúde; Inova Fiocruz/Fundação Oswaldo Cruz (Grants VPPCB-007-FIO-18–2–30 and VPPCB-005-FIO-20–2–87), INCT-FCx (465259/2014–6) and Fundação Carlos Chagas Filho de Amparo a` Pesquisa do Estado do Rio de Janeiro (26/210.196/2020). CNPq (306146/2017–7, 303902/2019–1, 302317/2017–1 and 313403/2018-0, respectively). FAPERJ (Grant number E-26/202.896/2018).Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, BrazilFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de AIDS e Imunologia Molecular. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Leônidas e Maria Deane Institute. Laboratório de Ecologia de Doenças Transmissíveis na Amazônia. Manaus, AM, BrazilFundação Oswaldo Cruz. Programa de Computação Científica. Grupo de Métodos Analíticos em Vigilância Epidemiológica. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, BrazilFundação Oswaldo Cruz. Instituto Aggeu Magalhães. Recife, PE, BrazilFundação Oswaldo Cruz. Instituto Aggeu Magalhães. Recife, PE, BrazilMinistério da Saúde. Secretaria de Vigilância em Saúde. Instituto Evandro Chagas. Ananindeua, PA, BrasilInstituto Adolfo Lutz. São Paulo, SP, BrazilSecretaria de Saúde de Aparecida de Goiânia. Goiás, GO, BrazilSecretaria de Saúde de Aparecida de Goiânia. Goiás, GO, BrazilLaboratório HLAGYN. Goiânia, GO, BrazilFundação Oswaldo Cruz . Fortaleza, CE, BrazilFundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, BrazilFundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, BrazilFundação Oswaldo Cruz. Instituto Aggeu Magalhães. Recife, PE, BrazilUniversidade Federal do Espirito Santo. Departamento de Biologia. Centro de Ciências Exatas, Naturais e da Saude. Espirito Santo, ES, BrazilOswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, BrazilOswaldo Cruz Foundation. Oswaldo Cruz Institute. Laboratory of Respiratory Viruses and Measles. Rio de Janeiro, RJ, BrazilThe COVID-19 epidemic in Brazil experienced two major lineage replacements until mid-2021. The first was driven by lineage P.2, in late 2020, and the second by lineage Gamma, in early 2021. To understand how these SARS-CoV-2 lineages spread in Brazil, we analyzed 11,724 genomes collected throughout the country between September 2020 and April 2021. Our findings indicate that lineage P.2 probably emerged in July 2020 in the Rio de Janeiro state and Gamma in November 2020 in the Amazonas state. Both states were the main hubs of viral disseminations to other Brazilian locations. We estimate that Gamma was 1.56-3.06 times more transmissible than P.2 in Rio de Janeiro and that the median effective reproductive number (Re) of Gamma varied according to the geographic context (Re = 1.59-3.55). In summary, our findings support that lineage Gamma was more transmissible and spread faster than P.2 in Brazil

Assessment of clinical characteristics and viral load in individuals infected by Delta and Omicron variants of SARS-CoV-2

In late 2021, a new variant of SARS-CoV-2 called Omicron emerged, replacing Delta worldwide. Although it has been associated with a lower risk of hospitalization and severe forms of COVID-19, there is little evidence of its relationship with specific symptoms and viral load. The aim of this study was to verify the relationship between Delta and Omicron variants of concern, viral load, and the occurrence of symptoms in individuals with COVID-19. Nasopharyngeal swab samples were collected and sequenced from patients with COVID-19 from the Northeast Region of Brazil between August 2021 and March 2022. The results showed a gradual replacement of the Delta variant by the Omicron variant during the study period. A total of 316 samples (157 Delta and 159 Omicron) were included. There was a higher prevalence of symptoms in Delta-infected individuals, such as coryza, olfactory and taste disturbances, headache, and myalgia. There was no association between viral load and the variants analyzed. The results reported here contribute to the understanding of the symptoms associated with the Delta and Omicron variants in individuals affected by COVID-19

SARS-CoV-2 intra-host diversity, antibody response, and disease severity after reinfection by the variant of concern Gamma in Brazil

Abstract The rapid spread of the SARS-CoV-2 Variant of Concern (VOC) Gamma in Amazonas during early 2021 fueled a second large COVID-19 epidemic wave and raised concern about the potential role of reinfections. Very few cases of reinfection associated with the VOC Gamma have been reported to date, and their potential impact on clinical, immunological, and virological parameters remains largely unexplored. Here we describe 25 cases of SARS-CoV-2 reinfection in Brazil. SARS-CoV-2 genomic analysis confirmed that individuals were primo-infected with distinct viral lineages between March and December 2020 (B.1.1, B.1.1.28, B.1.1.33, B.1.195, and P.2) and reinfected with the VOC Gamma between 3 to 12 months after primo-infection. We found a similar mean cycle threshold (Ct) value and limited intra-host viral diversity in both primo-infection and reinfection samples. Sera of 14 patients tested 10–75 days after reinfection displayed detectable neutralizing antibodies (NAb) titers against SARS-CoV-2 variants that circulated before (B.1.*), during (Gamma), and after (Delta and Omicron) the second epidemic wave in Brazil. All individuals had milder or no symptoms after reinfection, and none required hospitalization. These findings demonstrate that individuals reinfected with the VOC Gamma may display relatively high RNA viral loads at the upper respiratory tract after reinfection, thus contributing to onward viral transmissions. Despite this, our study points to a low overall risk of severe Gamma reinfections, supporting that the abrupt increase in hospital admissions and deaths observed in Amazonas and other Brazilian states during the Gamma wave was mostly driven by primary infections. Our findings also indicate that most individuals analyzed developed a high anti-SARS-CoV-2 NAb response after reinfection that may provide some protection against reinfection or disease by different SARS-CoV-2 variants