Abstract This study compares the effects of virus-cell interactions among SARS-CoV-2 variants of concern (VOCs) isolated in Brazil in 2021, hypothesizing a correlation between cellular alterations and mortality and between viral load and transmissibility. For this purpose, reference isolates of Alpha, Gamma, Zeta, and Delta variants were inoculated into monolayers of Vero-E6 cells. Viral RNA was quantified in cell supernatants by RT‒PCR, and infected cells were analyzed by Transmission Electron Microscopy (TEM) for qualitative and quantitative evaluation of cellular changes 24, 48, and 72 hours postinfection (hpi). Ultrastructural analyses showed that all variants of SARS-CoV-2 altered the structure and function of mitochondria, nucleus, and rough endoplasmic reticulum of cells. Monolayers infected with the Delta variant showed the highest number of modified cells and the greatest statistically significant differences compared to those of other variants. Viral particles were observed in the cytosol and the cell membrane in 100 % of the cells at 48 hpi. Alpha showed the highest mean particle diameter (79 nm), and Gamma and Delta were the smallest (75 nm). Alpha and Gamma had the highest particle frequency per field at 48 hpi, while the same was observed for Zeta and Delta at 72 hpi and 24 hpi, respectively. The cycle threshold of viral RNA varied among the target protein, VOC, and time of infection. The findings presented here demonstrate that all four VOCs evaluated caused ultrastructural changes in Vero-E6 cells, which were more prominent when infection occured with the Delta variant. viruscell virus SARSCoV2 SARSCoV SARS CoV 2 SARS-CoV- (VOCs 2021 transmissibility purpose VeroE6 VeroE Vero E6 E Vero-E RTPCR RT PCR RT‒PCR TEM (TEM 7 . (hpi) mitochondria nucleus 10 4 79 (7 nm, nm , nm) 75 nm. respectively protein VOC SARS-CoV 202 (hpi 1 ( 20

Abstract FioAntar, FIOCRUZ’s research project in Antarctica, is based on the One Health approach. FioAntar aims to generate relevant information that will help reduce the risk of future pandemics and improve the search for chemical compounds and new biological molecules. After four expeditions to Antarctica under the scope of PROANTAR, Fiocruz has identified Influenza H11N2 virus in environmental fecal samples, as well as Histoplasma capsulatum and Bacillus cereus in soil samples. In addition, in a prospective virome analysis from different lakes in the South Shetland Islands, six viral orders were described, supporting future research related to the biodiversity and viral ecology in this extreme ecosystem. Our findings of environmental pathogens of public health importance are a warning about the urgency of establishing a surveillance agenda on zoonoses in Antarctica due to the imminent risks that ongoing environmental and climate changes impose on human health across the planet. FioAntar strives to establish a comprehensive surveillance program across Antarctica, monitoring circulation of pathogens with the potential to transcend continent boundaries, thereby mitigating potential spread. For Fiocruz, Antarctica signifies a new frontier, teeming with opportunities to explore novel techniques, refine established methodologies, and cultivate invaluable knowledge. FIOCRUZs FIOCRUZ s approach molecules PROANTAR HN H N H11N samples addition Islands described ecosystem planet boundaries spread frontier techniques methodologies knowledge

Resumen: Desde mayo de 2020 se realiza un estudio exhaustivo con el fin de estimar el curso natural de la infección por SARS-CoV-2 en Río de Janeiro, Brasil. Se aplica un seguimiento a las familias en el cual se recolectan sistemáticamente muestras de sangre y de las vías respiratorias, se controlan los síntomas y se recogen datos sobre el estado de vacunación. Este artículo tiene como objetivo describir la cohorte de hogares durante cinco olas epidémicas de SARS-CoV-2, y proporcionar una visión general de los datos recopilados y una descripción de las características epidemiológicas, clínicas e inmunológicas, y de la incidencia de la infección por SARS-CoV-2. La cohorte incluyó a 691 participantes de 189 hogares. A lo largo de las cinco olas epidémicas, se detectaron 606 infecciones. La densidad de incidencia de la infección por SARS-CoV-2 varió de 4 (Delta) a 56 (B.1.1.33) por cada 1.000 personas por semana, y fue más alta en la ola B.1.1.33 en todos los grupos de edad. La seroprevalencia de anticuerpos contra el SARS-CoV-2 (proteína IgG antipico) varió del 37% en el período anti-VOC al 99% en el período Ómicron y aumentó ola tras ola de manera similar, independientemente de la edad de los participantes. El monitoreo continuo de la cohorte desde el comienzo de la pandemia permitió recopilar datos en diferentes escenarios según la cepa predominante en circulación. A partir del monitoreo activo de las familias, se realizó una vigilancia epidemiológica del SARS-CoV-2, sus variantes, la persistencia de los síntomas y los cambios en la inmunidad de la población a lo largo del tiempo, contribuyendo al conocimiento del curso natural de la infección por SARS-CoV-2. Resumen 202 SARSCoV2 SARSCoV SARS CoV 2 SARS-CoV- Janeiro Brasil respiratorias vacunación SARSCoV2, 2, epidemiológicas inmunológicas SARSCoV2. 2. 69 18 60 infecciones Delta (Delta 5 B1133 B 1 33 (B.1.1.33 1000 000 1.00 semana B.1.1.3 proteína antipico 37 antiVOC anti VOC 99 similar circulación variantes tiempo 20 SARS-CoV 6 B113 3 (B.1.1.3 100 00 1.0 B.1.1. 9 B11 (B.1.1. 10 0 1. B.1.1 B1 (B.1.1 B.1. (B.1. B.1 (B.1 B. (B. (B

Resumo: Desde maio de 2020, temos conduzido um estudo abrangente para entender a história natural da infecção por SARS-CoV-2 no Rio de Janeiro, Brasil. Nosso foco tem sido acompanhar as famílias das quais coletamos sistematicamente amostras de sangue e do trato respiratório, monitoramos os sintomas e reunimos dados sobre o status de vacinação. Este artigo tem como objetivo descrever a coorte de domicílios ao longo de cinco ondas epidêmicas de SARS-CoV-2, fornecendo uma visão geral dos dados coletados e uma descrição das características epidemiológicas, clínicas e imunológicas e da incidência da infecção por SARS-CoV-2. Nossa coorte inclui 691 participantes de 189 domicílios. Ao longo das cinco ondas epidêmicas, detectamos 606 infecções. A densidade de incidência da infecção por SARS-CoV-2 variou de 4 (Delta) a 56 (B.1.1.33) a cada 1.000 pessoas por semana e foi mais alta na onda B.1.1.33 em todas as faixas etárias. A soroprevalência de anticorpos contra o SARS-CoV-2 (proteína IgG anti-spike) variou de 37% no período pré-VoC a 99% no período Omicron e aumentou onda após onda de maneira semelhante, independentemente da idade dos participantes. Como monitoramos a coorte continuamente desde o início da pandemia, pudemos coletar dados em diferentes cenários, de acordo com a cepa predominante em circulação. Por meio do monitoramento ativo das famílias, conseguimos conduzir uma vigilância epidemiológica do SARS-CoV-2, de suas variantes, da persistência dos sintomas e das mudanças na imunidade da população ao longo do tempo, contribuindo para o conhecimento da história natural da infecção pelo SARS-CoV-2. Resumo 2020 SARSCoV2 SARSCoV SARS CoV 2 SARS-CoV- Janeiro Brasil respiratório vacinação SARSCoV2, 2, epidemiológicas SARSCoV2. 2. 69 18 60 infecções Delta (Delta 5 B1133 B 1 33 (B.1.1.33 1000 000 1.00 B.1.1.3 etárias proteína antispike anti spike anti-spike 37 préVoC pré VoC 99 semelhante pandemia cenários circulação variantes tempo 202 SARS-CoV 6 B113 3 (B.1.1.3 100 00 1.0 B.1.1. 9 20 B11 (B.1.1. 10 0 1. B.1.1 B1 (B.1.1 B.1. (B.1. B.1 (B.1 B. (B. (B

Abstract: Since May 2020, we have been conducting a comprehensive study to understand the natural history of SARS-CoV-2 infection in Rio de Janeiro, Brazil. Our focus has been on following families, systematically collecting respiratory tract swabs and blood samples, monitoring symptoms, and gathering data on vaccine status. This paper aims to describe the household cohort across five epidemic waves of SARS-CoV-2, providing an overview of the collected data and a description of the epidemiological, clinical, and immunological characteristics and incidence of SARS-CoV-2 infection. Our cohort includes 691 participants from 189 households. During the five epidemic waves, we detected 606 infections. The incidence density of SARS-CoV-2 infection ranged from 4 (Delta) to 56 (B.1.1.33) per 1,000 person-week, with a peak in wave B.1.1.33 in all age groups. The seroprevalence of SARS-CoV-2 antibodies (IgG anti spike protein) varied from 37%, in the pre-VoC period, to 99%, in the Omicron period, progressively increasing after each wave in a similar manner regardless of age. As we have monitored the cohort continuously since the beginning of the pandemic, we were able to collect data across different scenarios according to the predominant lineage in circulation. Via active monitoring of families, we were able to carry out an epidemiological surveillance on SARS-CoV-2, including its variants, persistence of symptoms, and changes in immunity over time in the population, contributing to knowledge of the natural history of SARS-CoV-2 infection. Abstract 2020 SARSCoV2 SARSCoV SARS CoV 2 SARS-CoV- Janeiro Brazil families samples symptoms status SARSCoV2, 2, clinical 69 18 households 60 infections Delta (Delta 5 B1133 B 1 33 (B.1.1.33 1000 000 1,00 personweek, personweek person week, week person-week B.1.1.3 groups IgG protein 37 37% preVoC pre VoC period 99 99% pandemic circulation variants population 202 SARS-CoV 6 B113 3 (B.1.1.3 100 00 1,0 B.1.1. 9 20 B11 (B.1.1. 10 0 1, B.1.1 B1 (B.1.1 B.1. (B.1. B.1 (B.1 B. (B. (B

BACKGROUND In response to the coronavirus disease 2019 (Covid-19) pandemic, Brazil authorised the Astra Zeneca/Fiocruz vaccine in January 2021. As the Delta variant emerged in May 2021, interval between vaccine doses was adjusted. By September 2021, the Brazilian National Immunisation Program recommended a booster dose for individuals over 70, and later expanded the recommendation to all adults. OBJECTIVES Assess the equivalence of IgG antibody response against the Covid-19 S protein before and approximately 28 days after the third dose of a Covid-19 recombinant vaccine. Two groups received initial two doses with intervals of eight and 12 weeks. METHODS This is a phase IV clinical study, uncontrolled, non-randomised. The study proposes calculating the ratio of geometric means titres (GMT) 28 days after the third dose, with a target ratio of confidence interval (CI) between 0.77 and 1.3. FINDINGS In the primary endpoint, there was no equivalence between the eight- and 12-week intervals with a slight variation favouring the eight-week group. Post-third dose, both groups showed increases titres at 28 days, three months, six months and 12 months. Both groups responded similarly to Delta and Omicron BA.1, with a more significant increase for Delta. MAIN CONCLUSIONS The study showed strong and consistent immune response in all age groups receiving the Covid-19 recombinant vaccine. Third dose elicited an increase in GMT by at least three times aligned with Ministry of Health strategies emphasising Bio-Manguinhos crucial role in pandemic control in the country. 201 Covid19 Covid 19 (Covid-19 ZenecaFiocruz Zeneca Fiocruz 2021 adjusted 70 adults Covid-1 2 1 weeks uncontrolled nonrandomised. nonrandomised non randomised. randomised non-randomised (GMT CI (CI 077 0 77 0.7 13 3 1.3 endpoint 12week week eightweek group Postthird Post BA1 BA BA.1 BioManguinhos Bio Manguinhos country 20 Covid1 (Covid-1 202 7 Covid- 07 0. 1. BA. (Covid- (Covid

Resumen: Desde mayo de 2020 se realiza un estudio exhaustivo con el fin de estimar el curso natural de la infección por SARS-CoV-2 en Río de Janeiro, Brasil. Se aplica un seguimiento a las familias en el cual se recolectan sistemáticamente muestras de sangre y de las vías respiratorias, se controlan los síntomas y se recogen datos sobre el estado de vacunación. Este artículo tiene como objetivo describir la cohorte de hogares durante cinco olas epidémicas de SARS-CoV-2, y proporcionar una visión general de los datos recopilados y una descripción de las características epidemiológicas, clínicas e inmunológicas, y de la incidencia de la infección por SARS-CoV-2. La cohorte incluyó a 691 participantes de 189 hogares. A lo largo de las cinco olas epidémicas, se detectaron 606 infecciones. La densidad de incidencia de la infección por SARS-CoV-2 varió de 4 (Delta) a 56 (B.1.1.33) por cada 1.000 personas por semana, y fue más alta en la ola B.1.1.33 en todos los grupos de edad. La seroprevalencia de anticuerpos contra el SARS-CoV-2 (proteína IgG antipico) varió del 37% en el período anti-VOC al 99% en el período Ómicron y aumentó ola tras ola de manera similar, independientemente de la edad de los participantes. El monitoreo continuo de la cohorte desde el comienzo de la pandemia permitió recopilar datos en diferentes escenarios según la cepa predominante en circulación. A partir del monitoreo activo de las familias, se realizó una vigilancia epidemiológica del SARS-CoV-2, sus variantes, la persistencia de los síntomas y los cambios en la inmunidad de la población a lo largo del tiempo, contribuyendo al conocimiento del curso natural de la infección por SARS-CoV-2.

Resumo: Desde maio de 2020, temos conduzido um estudo abrangente para entender a história natural da infecção por SARS-CoV-2 no Rio de Janeiro, Brasil. Nosso foco tem sido acompanhar as famílias das quais coletamos sistematicamente amostras de sangue e do trato respiratório, monitoramos os sintomas e reunimos dados sobre o status de vacinação. Este artigo tem como objetivo descrever a coorte de domicílios ao longo de cinco ondas epidêmicas de SARS-CoV-2, fornecendo uma visão geral dos dados coletados e uma descrição das características epidemiológicas, clínicas e imunológicas e da incidência da infecção por SARS-CoV-2. Nossa coorte inclui 691 participantes de 189 domicílios. Ao longo das cinco ondas epidêmicas, detectamos 606 infecções. A densidade de incidência da infecção por SARS-CoV-2 variou de 4 (Delta) a 56 (B.1.1.33) a cada 1.000 pessoas por semana e foi mais alta na onda B.1.1.33 em todas as faixas etárias. A soroprevalência de anticorpos contra o SARS-CoV-2 (proteína IgG anti-spike) variou de 37% no período pré-VoC a 99% no período Omicron e aumentou onda após onda de maneira semelhante, independentemente da idade dos participantes. Como monitoramos a coorte continuamente desde o início da pandemia, pudemos coletar dados em diferentes cenários, de acordo com a cepa predominante em circulação. Por meio do monitoramento ativo das famílias, conseguimos conduzir uma vigilância epidemiológica do SARS-CoV-2, de suas variantes, da persistência dos sintomas e das mudanças na imunidade da população ao longo do tempo, contribuindo para o conhecimento da história natural da infecção pelo SARS-CoV-2.

Abstract: Since May 2020, we have been conducting a comprehensive study to understand the natural history of SARS-CoV-2 infection in Rio de Janeiro, Brazil. Our focus has been on following families, systematically collecting respiratory tract swabs and blood samples, monitoring symptoms, and gathering data on vaccine status. This paper aims to describe the household cohort across five epidemic waves of SARS-CoV-2, providing an overview of the collected data and a description of the epidemiological, clinical, and immunological characteristics and incidence of SARS-CoV-2 infection. Our cohort includes 691 participants from 189 households. During the five epidemic waves, we detected 606 infections. The incidence density of SARS-CoV-2 infection ranged from 4 (Delta) to 56 (B.1.1.33) per 1,000 person-week, with a peak in wave B.1.1.33 in all age groups. The seroprevalence of SARS-CoV-2 antibodies (IgG anti spike protein) varied from 37%, in the pre-VoC period, to 99%, in the Omicron period, progressively increasing after each wave in a similar manner regardless of age. As we have monitored the cohort continuously since the beginning of the pandemic, we were able to collect data across different scenarios according to the predominant lineage in circulation. Via active monitoring of families, we were able to carry out an epidemiological surveillance on SARS-CoV-2, including its variants, persistence of symptoms, and changes in immunity over time in the population, contributing to knowledge of the natural history of SARS-CoV-2 infection.

BACKGROUND The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) has changed unevenly over time around the world. Although whole genome sequencing is the gold standard for virus characterisation, the discovery of alpha VOC causing spike gene target failure (SGTF) result, when tested using an reverse transcription real-time polymerase chain reaction (RT-qPCR) assay, has provided a simple tool for tracking the frequencies of variants. OBJECTIVES The aim of this study was to investigate if a multiplex RT-qPCR assay (BioM 4Plex VOC) could be used to detect SARS-CoV-2 and to perform a VOC screening test in a single reaction tube. Here, we present the multicentre study evaluating this assay. METHODS Twelve laboratories have participated in the multicentre study. The BioM 4Plex VOC was distributed to them with detailed instructions of how to perform the test. They were asked to test the BioM 4Plex VOC in parallel with their routine Commercial SARS-CoV-2 diagnostic assay. Additionally, they were requested to select SARS-CoV-2-positive samples with genome sequenced and lineage definition according to PANGO lineage classification. FINDINGS The BioM 4Plex VOC and commercial RT-PCR assay are equally effective in detecting SARS-CoV-2. Results revealed a specificity of 96.5-100% [95% confidence interval (CI)], a sensitivity of 99.8-100% (95% CI), and an accuracy of 99.8-100% (95% CI). A 99% concordance rate was found between results from the BioM 4Plex VOC and that from available genome sequencing data. MAIN CONCLUSIONS The BioM 4Plex VOC provides an effective solution to detect SARS-CoV-2 infections and screening for VOCs in a single reaction. It is a straightforward method to help us monitor the frequency and distribution of VOCs and develop strategies to better cope with the pandemics. SARSCoV2 SARSCoV SARS CoV (SARS-CoV-2 (VOCs world characterisation SGTF (SGTF result realtime real RTqPCR RT qPCR (RT-qPCR Plex SARS-CoV- tube Here Additionally SARSCoV2positive SARSCoVpositive positive classification RTPCR PCR SARSCoV2. 2. 96.5100% 965100 96.5 100% 96 5 100 96.5-100 95% 95 [95 CI, CI , (CI)] 99.8100% 998100 99.8 99 8 99.8-100 (95 CI) CI. . data pandemics (SARS-CoV- SARS-CoV 5100 96.5100 96510 965 96. 9 10 96.5-10 [9 (CI) 8100 99.8100 99810 998 99. 99.8-10 (9 (SARS-CoV 510 96.510 9651 1 96.5-1 [ (CI 810 99.810 9981 99.8-1 ( 51 96.51 96.5- 81 99.81 99.8-

BACKGROUND There is interest in lingering non-specific symptoms after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, referred to as Long coronavirus disease 2019 (Long COVID-19). It remains unknown whether the risk of Long COVID-19 is associated with pre-existing comorbidities or initial COVID-19 severity, including infections due to new Omicron lineages which predominated in 2023. OBJECTIVES The aim of this case report was to characterize the clinical features of acute XBB.1.5 infection followed by Long COVID-19. METHODS We followed a 73-year old female resident of Rio de Janeiro with laboratory-confirmed SARS-CoV-2 during acute infection and subsequent months. The SARS-CoV-2 lineage was determined by genome sequencing. FINDINGS The participant denied comorbidities and had completed a two-dose vaccination schedule followed by two booster doses eight months prior to SARS-CoV-2 infection. Primary infection by viral lineage XBB.1.5. was clinically mild, but the participant subsequently reported persistent fatigue. MAIN CONCLUSIONS This case demonstrates that Long COVID-19 may develop even after mild disease due to SARS-CoV-2 in fully vaccinated and boosted individuals without comorbidities. Continued monitoring of new SARS-CoV-2 lineages and associated clinical outcomes is warranted. Measures to prevent infection should continue to be implemented including development of new vaccines and antivirals effective against novel variants. nonspecific non specific SARSCoV2 SARSCoV SARS CoV (SARS-CoV-2 201 COVID19. COVID19 COVID 19 . COVID-19) COVID-1 preexisting pre existing severity 2023 XBB15 XBB 1 5 XBB.1. 19. 73year year 73 laboratoryconfirmed laboratory confirmed SARS-CoV- sequencing twodose dose fatigue warranted variants (SARS-CoV- 20 COVID1 COVID- 202 XBB1 XBB.1 7 SARS-CoV (SARS-CoV XBB.

Abstract Numerous Antarctic species are recognized as reservoirs for various pathogens, and their migratory behavior allows them to reach the Brazilian coast, potentially contributing to the emergence and circulation of new infectious diseases. To address the potential zoonotic risks, we conducted surveillance of influenza A virus (IAV) and coronaviruses (CoVs) in the Antarctic Peninsula, specifically focusing on different bird and mammal species in the region. During the summer of 2021/2022, as part of the Brazilian Antarctic Expedition, we collected and examined a total of 315 fecal samples to target these respiratory viruses. Although we did not detect the viruses of interest during this particular expedition, previous research conducted by our team has shown the presence of the H11N2 subtype of influenza A virus in penguin fecal samples from the same region. Given the continuous emergence of new viral strains worldwide, it is crucial to maintain active surveillance in the area, contributing to strengthening integrated One Health surveillance efforts. pathogens coast diseases risks IAV (IAV CoVs (CoVs Peninsula region 20212022 2021 2022 2021/2022 Expedition 31 expedition HN H N H11N worldwide area efforts 2021202 202 2021/202 3 202120 20 2021/20 20212 2 2021/2 2021/

RESUMO O Município do Rio de Janeiro (MRJ) estava entre as cidades com altas taxas de mortalidade ao longo da pandemia de Covid-19. Neste estudo, analisamos as taxas de incidência, de mortalidade e letalidade por Covid-19 nas áreas com predominância de Aglomerados Subnormais (ASN). Foram considerados todos os 36 bairros da Sub-Bacia do Canal do Cunha (SBCC) associadas às características demográficas, socioeconômicas e epidemiológicas, com estatística espacial de Moran. A taxa de incidência nos bairros da SBCC foi de 621,5/10.000 habitantes. Complexo do Alemão, Mangueira, e Maré tiveram maiores proporções de casos e mortes. A menor incidência (33,6/10.000 habitantes) e mortalidade (8,3/10.000 habitantes), mas com maior taxa de letalidade (24,7%) foi registrada no Complexo do Alemão. Foi observado correlação negativa entre a taxa de mortalidade e a proporção de habitantes nos bairros com ASN (rho= -0,433; p=0,023). Na estatística espacial, houve correlação inversa para a incidência da Covid-19 (índice Moran, -0,155863; p=0,02). Conclui-se que incidência e mortalidade nas áreas de ASN estão significativamente relacionadas com as estruturas sociodemográficas, demandando o reforço dos sistemas de vigilância e de controle da Covid-19 em territórios de favelas. As recomendações não farmacológicas e a Atenção Primária à Saúde em favelas desempenham relevante papel na redução da transmissão, mortalidade e iniquidades em saúde.

ABSTRACT Along COVID-19 pandemics, Rio de Janeiro (MRJ) has figured among the Brazilian cities with the highest mortality rates. In this study, we explored COVID-19 incidence and mortality in areas with a predominance of subnormal population clusters (SNC) in MRJ. We analyzed 36 neighborhoods of Canal do Cunha Sub-basin (CCSB) and the associations between demographic, socioeconomic, and epidemiological features, and the cumulative incidence, mortality, and lethality rates, and Moran’s spatial statistics were performed. The incidence rate in CCSB neighborhoods was 621.5/10,000 inhabitants. Complexo do Alemão, Mangueira, and Maré had the highest proportions of cases and deaths. And the lowest incidence (33.6/10,000 inhabitants), mortality (8.3/10,000 inhabitants), but with the highest lethality rate (24.7%) was recorded in Complexo do Alemão. There was a negative correlation between mortality and the proportion of inhabitants in neighborhoods with ASN (rho= -0.433; p=0.023). In spatial statistics, there was an inverse correlation for the incidence (Moran index, -0.155863; p=0.02). It is concluded that incidence and mortality in SNC areas are significantly related to their sociodemographic structures, highlighting the need to strengthen the surveillance and control systems of COVID-19 in slums territories. Non-pharmacological recommendations and suitable Primary Health Care in slums areas play a relevant role in reducing viral transmission, mortality, and health inequities.

RESUMO O Município do Rio de Janeiro (MRJ) estava entre as cidades com altas taxas de mortalidade ao longo da pandemia de Covid-19. Neste estudo, analisamos as taxas de incidência, de mortalidade e letalidade por Covid-19 nas áreas com predominância de Aglomerados Subnormais (ASN). Foram considerados todos os 36 bairros da Sub-Bacia do Canal do Cunha (SBCC) associadas às características demográficas, socioeconômicas e epidemiológicas, com estatística espacial de Moran. A taxa de incidência nos bairros da SBCC foi de 621,5/10.000 habitantes. Complexo do Alemão, Mangueira, e Maré tiveram maiores proporções de casos e mortes. A menor incidência (33,6/10.000 habitantes) e mortalidade (8,3/10.000 habitantes), mas com maior taxa de letalidade (24,7%) foi registrada no Complexo do Alemão. Foi observado correlação negativa entre a taxa de mortalidade e a proporção de habitantes nos bairros com ASN (rho= -0,433; p=0,023). Na estatística espacial, houve correlação inversa para a incidência da Covid-19 (índice Moran, -0,155863; p=0,02). Conclui-se que incidência e mortalidade nas áreas de ASN estão significativamente relacionadas com as estruturas sociodemográficas, demandando o reforço dos sistemas de vigilância e de controle da Covid-19 em territórios de favelas. As recomendações não farmacológicas e a Atenção Primária à Saúde em favelas desempenham relevante papel na redução da transmissão, mortalidade e iniquidades em saúde.

ABSTRACT Along COVID-19 pandemics, Rio de Janeiro (MRJ) has figured among the Brazilian cities with the highest mortality rates. In this study, we explored COVID-19 incidence and mortality in areas with a predominance of subnormal population clusters (SNC) in MRJ. We analyzed 36 neighborhoods of Canal do Cunha Sub-basin (CCSB) and the associations between demographic, socioeconomic, and epidemiological features, and the cumulative incidence, mortality, and lethality rates, and Moran’s spatial statistics were performed. The incidence rate in CCSB neighborhoods was 621.5/10,000 inhabitants. Complexo do Alemão, Mangueira, and Maré had the highest proportions of cases and deaths. And the lowest incidence (33.6/10,000 inhabitants), mortality (8.3/10,000 inhabitants), but with the highest lethality rate (24.7%) was recorded in Complexo do Alemão. There was a negative correlation between mortality and the proportion of inhabitants in neighborhoods with ASN (rho= -0.433; p=0.023). In spatial statistics, there was an inverse correlation for the incidence (Moran index, -0.155863; p=0.02). It is concluded that incidence and mortality in SNC areas are significantly related to their sociodemographic structures, highlighting the need to strengthen the surveillance and control systems of COVID-19 in slums territories. Non-pharmacological recommendations and suitable Primary Health Care in slums areas play a relevant role in reducing viral transmission, mortality, and health inequities.

BACKGROUND The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become a major concern contributing to increased morbidity and mortality worldwide. OBJECTIVES Here we describe the replacement of the Gamma variant of concern (VOC) with Delta in the western Brazilian Amazon. METHODS In this study, we analysed 540 SARS-CoV-2 positive samples determined by qualitative real-time RT-PCR selected in the state of Rondônia between June and December 2021. The positive cohort was sequenced through next-generation sequencing (NGS) and each sample was quantified using real-time RT-qPCR, the whole genome sequence was obtained, SARS-CoV-2 lineages were classified using the system Pango and the maximum likelihood (ML) method was used to conduct phylogenetic analyses. FINDINGS A total of 540 high-quality genomes were obtained, where the Delta VOC showed the highest prevalence making up 72%, with strain AY.43 being the most abundant, while the Gamma VOC was present in 28%, where the P.1 strain was the most frequent. In this study population, only 32.96% (178/540) had completed the vaccination schedule. MAIN CONCLUSIONS This study highlighted the presence of Gamma and Delta variants of SARS-CoV-2 in RO. Furthermore, we observed the replacement of the Gamma VOC with the Delta VOC and its lineages. SARSCoV2 SARSCoV SARS CoV (SARS-CoV-2 worldwide (VOC Amazon 54 SARS-CoV- realtime real time RTPCR RT PCR 2021 nextgeneration next generation NGS (NGS RTqPCR, RTqPCR qPCR, qPCR RT-qPCR obtained ML (ML analyses highquality high quality 72 72% AY43 AY 43 AY.4 abundant 28 28% P1 P 1 P. frequent population 3296 32 96 32.96 178/540 178540 178 (178/540 schedule RO Furthermore (SARS-CoV- 5 SARS-CoV 202 7 AY4 4 AY. 329 3 9 32.9 178/54 17854 17 (178/54 (SARS-CoV 20 32. 178/5 1785 (178/5 178/ (178/ (178 (17 (1 (

The objective of this study was to analyze the COVID-19 incidence of and mortality in a population from a territorial area with a predominance of neighborhoods with slum areas (subnormal settlements), and its relationship with contextual variables. We analyzed 36 neighborhoods of the Canal do Cunha Sub-basin that presented 30,008 deaths by COVID-19 until February 5, 2021. Cumulative incidence, cumulative mortality, and cumulative lethality rates were considered as dependent variables. Contextual variables included patient neighborhood; proportion of ASN by neighborhoods, percentage of black and brown people, age group; income ratio, and sanitation indices. The variables were analyzed descriptively, bivariately by Spearman correlation, and Moran's spatial statistics were performed. The Complexo do Alemão, Mangueira, and Maré neighborhoods had the highest proportions of cases and deaths from COVI-19. The percentage of infection in the 20 to 29, 30 to 39, and 40 to 49 age groups were 13.6%, 21.5%, and 20.1%, respectively. In the 70 to 79 age group was 7.3% of the total COVID-19 cases, and 26.7% deaths and 34.2% lethality rate. When added the records of black and brown people with those without records for color/race there was significant positive moderate correlation between the cumulative incidence rate and mortality rate (rho = 0.383; p=0.048 and rho= 0.3176; p= 0.0106). The global and local Moran's spatial statistical evaluation allowed to verify intermediate and medium priority areas that need to strengthen the surveillance and control system of COVID-19. The epidemiological situation of an area with a high percentage of slum areas showed that mortality by COVID-19 in black and brown people is related to demographic aspects and that there is low notification of cases and deaths attributed to COVID-19 in residents of areas with slums.

Objetivo desse estudo foi analisar a incidência e mortalidade por COVID-19 em população de área territorial com predominância de bairros com áreas de favelas (aglomerados subnormais), e sua relação com variáveis contextuais. Foram analisados 36 bairros da Sub-bacia do Canal do Cunha que apresentaram 30.008 óbitos por COVID-19 até o dia 05 de fevereiro de 2021. Considerou-se como variáveis dependentes as taxas de incidência acumulada, mortalidade acumulada e letalidade acumulada. Entre as variáveis contextuais, foram incluídas bairro do paciente; proporção de ASN por bairros, percentual de pretos e pardos, faixa etária; razão de renda, e índices de saneamento. As variáveis foram analisadas de forma descritiva, bivariada pela correlação de Spearman e utilizado a estatística espacial de Moran. Os bairros Complexo do Alemão, Mangueira e Maré foram que apresentaram as maiores proporções de casos e óbitos por COVI-19. O percentual de infecção nas faixas de 20 a 29 anos, 30 a 39 anos e 40 a 49 anos foram de 13,6%, 21.5% e 20,1%, respectivamente. Na faixa etária entre 70 e 79 anos foi 7,3% do total de casos de COVID-19, e 26,7% nbsp;de óbitos e 34,2% taxa de letalidade. Quando somado os registros de pessoas pretas e parda com os sem registro para cor/raça houve correlação moderada positiva significativa entre a taxa de incidência acumulada e a taxa de mortalidade nbsp;(rho = 0,383; p=0,048 e rho= 0,3176; p=0,0106). A avaliação estatística espacial global e local de Moran permitiu verificar áreas de prioridade intermediárias e médias que necessitam reforçar o sistema de vigilância e controle da COVID-19. A situação epidemiológica de área com grande percentual de áreas favelas mostrou que a mortalidade por COVID-19 em pessoas pretas e pardas está relacionada a aspectos demográficos e que ocorre baixa notificação de casos e de óbitos atribuídas ao COVID-19 em moradores de áreas com favelas.

BACKGROUND The coronaviruses (CoVs) called the attention of the world for causing outbreaks of severe acute respiratory syndrome (SARS-CoV), in Asia in 2002-03, and respiratory disease in the Middle East (MERS-CoV), in 2012. In December 2019, yet again a new coronavirus (SARS-CoV-2) first identified in Wuhan, China, was associated with a severe respiratory infection, known today as COVID-19. This new virus quickly spread throughout China and 30 additional countries. As result, the World Health Organization (WHO) elevated the status of the COVID-19 outbreak from emergency of international concern to pandemic on March 11, 2020. The impact of COVID-19 on public health and economy fueled a worldwide race to approve therapeutic and prophylactic agents, but so far, there are no specific antiviral drugs or vaccines available. In current scenario, the development of in vitro systems for viral mass production and for testing antiviral and vaccine candidates proves to be an urgent matter. OBJECTIVE The objective of this paper is study the biology of SARS-CoV-2 in Vero-E6 cells at the ultrastructural level. METHODS In this study, we documented, by transmission electron microscopy and real-time reverse transcription polymerase chain reaction (RT-PCR), the infection of Vero-E6 cells with SARS-CoV-2 samples isolated from Brazilian patients. FINDINGS The infected cells presented cytopathic effects and SARS-CoV-2 particles were observed attached to the cell surface and inside cytoplasmic vesicles. The entry of the virus into cells occurred through the endocytic pathway or by fusion of the viral envelope with the cell membrane. Assembled nucleocapsids were verified inside rough endoplasmic reticulum cisterns (RER). Viral maturation seemed to occur by budding of viral particles from the RER into smooth membrane vesicles. MAIN CONCLUSIONS Therefore, the susceptibility of Vero-E6 cells to SARS-CoV-2 infection and the viral pathway inside the cells were demonstrated by ultrastructural analysis.

BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.33-derived lineage named N.9 was described recently in Brazil and it’s considered a potential variant of interest (VOI) due to the presence of E484K substitution at the receptor-binding domain (RBD) of the Spike (S) protein. OBJECTIVE To describe the first detection of variant N.9 in Rio de Janeiro State. METHODS SARS-CoV-2 N.9 was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR), whole-genome sequencing and phylogenetic analysis. FINDINGS Here, we report two SARS-CoV-2 N.9 lineage strains in Rio de Janeiro. One of them had only the E484K substitution of the six N.9 lineage-defining mutations. Other three strains pre-defined as N.9 have the same genomic profile. These four strains are grouped within the B.1.1.33 lineage and basal to the N.9 lineage in our phylogenetic analysis, and we call them “N.9-like/B.1.1.33 + E484K”. MAIN CONCLUSIONS The phylogenetic analysis shows four independent introductions of N.9 in the state of Rio de Janeiro in October and December 2020, January and March 2021. SARS-CoV-2 N.9 dissemination in the Rio de Janeiro could have been limited by the emergence and dominance of other variants, mainly by the lineage P.2 VOI Zeta that emerged in the same period and co-circulated with N.9, as observed in the neighboring State of São Paulo.

Coronavirus disease 2019 (COVID-19) surveillance, in Brazil, initiated shortly after its description, in China. Our aim was to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and additional pathogens in samples from the initial phase of the outbreak in Brazil, from late February to late March. From 707 samples analysed, 29 (4.1%) were SARS-CoV-2 positive. Fever and cough were their most prevalent symptoms. Co-detection of rhinovirus was observed in 2 (6.9%) cases. Additional pathogens were identified in 66.1% of the SARS-CoV-2 negative cases, mainly rhinovirus and influenza A(H1N1)pdm09. Thus, we emphasise the importance of differential diagnosis in COVID-19 suspected cases.