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

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.

Inflammasome genes polymorphisms are associated with progression to mechanical ventilation and death in a cohort of hospitalized COVID-19 patients in a reference hospital in Rio de Janeiro, Brazil.

COVID-19 has a broad spectrum of clinical manifestations. We assessed the impact of single nucleotide polymorphisms (SNPs) of inflammasome genesas risk factors for progression toCOVID-19 critical outcomes, such as mechanical ventilation support (MVS) or death.The study included 451 hospitalized individuals followed up at the INI/FIOCRUZ, Rio de Janeiro, Brazil, from 06/2020 to 03/2021. SNPs genotyping was determined by Real-Time PCR. We analyzed risk factors for progression to MVS (n = 174[38.6 %]) or death (n = 175[38.8 %])as a result of COVID-19 by Cox proportional hazardmodels.Slower progression toMVSwas associated with allele G (aHR = 0.66;P = 0.005) or the genotype G/G (aHR = 0.391;P = 0.006) in the NLRP3 rs10754558 or the allele G (aHR = 0.309;P = 0.004) in the IL1ßrs1143634, while C allele in the NLRP3 rs4612666 (aHR = 2.342;P = 0.006) or in the rs10754558 (aHR = 2.957;P = 0.005) were associated with faster progression to death. Slower progression to death was associated to allele G (aHR = 0.563;P = 0.006) or the genotype A/G (aHR = 0.537;P = 0.005) in the CARD8 rs6509365; the genotype A/C in the IFI16 rs1101996 (aHR = 0.569;P = 0.011); the genotype T/T (aHR = 0.394;P = 0.004) or allele T (aHR = 0.68;P = 0.006) in the NLRP3 rs4612666, and the genotype G/G (aHR = 0.326;P = 0.005) or allele G (aHR = 0,68;P = 0.014) in the NLRP3 rs10754558. Our results suggest that inflammasome genetic variations might influence the critical clinical course of COVID-19.

The Impact of COVID-19 on HIV Care in Rio de Janeiro, Brazil 2019-2021: Disparities by Age and Gender.

We evaluated COVID-19's impact on HIV care indicators among INI/FIOCRUZ's HIV Clinical Cohort in Rio de Janeiro, Brazil: (1) Adequate care visits: two visits ≥ 90 days apart; (2) Adequate viral load monitoring: ≥ 2 viral load results ≥ 90 days apart; (3) Consistent viral suppression: all viral loads < 40 copies/mL; and (4) ART medication possession ratio (MPR) ≥ 95%. Chi-square tests compared the fraction of participants meeting each indicator per period: pre-pandemic (3/1/2019-2/29/2020) and post-pandemic (3/1/2020-2/28/2021). Logistic regression models were used to assess disparities in adequate care visits. Among 906 participants, care visits and viral load monitoring decreased pre-pandemic to post-pandemic: 77.0-55.1% and 36.6-11.6% (both p < 0.001), respectively. The optimal MPR rate improved from 25.5 to 40.0% (p < 0.001). Post-pandemic period (aOR 0.33, CI 0.28-0.40), transgender women (aOR 0.34, CI 0.22-0.53), and those aged 18-24 years (aOR 0.67, CI 0.45-0.97) had lower odds of adequate care visits. COVID-19 disrupted care access disproportionately for transgender women and younger participants.

Inflammasome Genetic Variants Are Associated with Protection to Clinical Severity of COVID-19 among Patients from Rio de Janeiro, Brazil.

COVID-19 has a broad spectrum of clinical manifestations, from asymptomatic or mild/moderate symptoms to severe symptoms and death. The mechanisms underlying its clinical evolution are still unclear. Upon SARS-CoV-2 infection, host factors, such as the inflammasome system, are activated by the presence of the virus inside host cells. The search for COVID-19 risk factors is of relevance for clinical management. In this study, we investigated the impact of inflammasome single-nucleotide polymorphisms (SNPs) in SARS-CoV-2-infected individuals with distinct severity profiles at clinical presentation. Patients were divided into two groups according to disease severity at clinical presentation based on the WHO Clinical Progression Scale. Group 1 included patients with mild/moderate disease (WHO < 6; n = 76), and group 2 included patients with severe/critical COVID-19 (WHO ≥ 6; n = 357). Inpatients with moderate to severe/critical profiles were recruited and followed-up at Hospital Center for COVID-19 Pandemic - National Institute of Infectology (INI)/FIOCRUZ, RJ, Brazil, from June 2020 to March 2021. Patients with mild disease were recruited at Oswaldo Cruz Institute (IOC)/FIOCRUZ, RJ, Brazil, in August 2020. Genotyping of 11 inflammasome SNPs was determined by real-time PCR. Protection and risk estimation were performed using unconditional logistic regression models. Significant differences in NLRP3 rs1539019 and CARD8 rs2043211 were observed between the two groups. Protection against disease severity was associated with the A/A genotype (ORadj = 0.36; P = 0.032), allele A (ORadj = 0.93; P = 0.010), or carrier-A (ORadj = 0.45; P = 0.027) in the NLRP3 rs1539019 polymorphism; A/T genotype (ORadj = 0.5; P = 0.045), allele T (ORadj = 0.93; P = 0.018), or carrier-T (ORadj = 0.48; P = 0.029) in the CARD8 rs2043211 polymorphism; and the A-C-G-C-C (ORadj = 0.11; P = 0.018), A-C-G-C-G (ORadj = 0.23; P = 0.003), C-C-G-C-C (ORadj = 0.37; P = 0.021), and C-T-G-A-C (ORadj = 0.04; P = 0.0473) in NLRP3 genetic haplotype variants. No significant associations were observed for the other polymorphisms. To the best of our knowledge, this is the first study demonstrating an association between CARD8 and NLRP3 inflammasome genetic variants and protection against COVID-19 severity, contributing to the discussion of the impact of inflammasomes on COVID-19 outcomes.

Prevalence and predictors of anti-SARS-CoV-2 serology in a highly vulnerable population of Rio de Janeiro: A population-based serosurvey.

Background: COVID-19 serosurveys allow for the monitoring of the level of SARS-CoV-2 transmission and support data-driven decisions. We estimated the seroprevalence of anti-SARS-CoV-2 antibodies in a large favela complex in Rio de Janeiro, Brazil. Methods: A population-based panel study was conducted in Complexo de Manguinhos (16 favelas) with a probabilistic sampling of participants aged ≥1 year who were randomly selected from a census of individuals registered in primary health care clinics that serve the area. Participants answered a structured interview and provided blood samples for serology. Multilevel regression models (with random intercepts to account for participants' favela of residence) were used to assess factors associated with having anti-S IgG antibodies. Secondary analyses estimated seroprevalence using an additional anti-N IgG assay. Findings: 4,033 participants were included (from Sep/2020 to Feb/2021, 22 epidemic weeks), the median age was 39·8 years (IQR:21·8-57·7), 61% were female, 41% were mixed-race (Pardo) and 23% Black. Overall prevalence was 49·0% (95%CI:46·8%-51·2%) which varied across favelas (from 68·3% to 31·4%). Lower prevalence estimates were found when using the anti-N IgG assay. Odds of having anti-S IgG antibodies were highest for young adults, and those reporting larger household size, poor adherence to social distancing and use of public transportation. Interpretation: We found a significantly higher prevalence of anti-S IgG antibodies than initially anticipated. Disparities in estimates obtained using different serological assays highlight the need for cautious interpretation of serosurveys estimates given the heterogeneity of exposure in communities, loss of immunological biomarkers, serological antigen target, and variant-specific test affinity. Funding: Fundação Oswaldo Cruz, Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ), the European Union's Horizon 2020 research and innovation programme, Royal Society, Serrapilheira Institute, and FAPESP.

In-hospital mortality and severe outcomes after hospital discharge due to COVID-19: A prospective multicenter study from Brazil.

Background: We evaluated in-hospital mortality and outcomes incidence after hospital discharge due to COVID-19 in a Brazilian multicenter cohort. Methods: This prospective multicenter study (RECOVER-SUS, NCT04807699) included COVID-19 patients hospitalized in public tertiary hospitals in Brazil from June 2020 to March 2021. Clinical assessment and blood samples were performed at hospital admission, with post-hospital discharge remote visits. Hospitalized participants were followed-up until March 31, 2021. The outcomes were in-hospital mortality and incidence of rehospitalization or death after hospital discharge. Kaplan-Meier curves and Cox proportional-hazard models were performed. Findings: 1589 participants [54.5% male, age=62 (IQR 50-70) years; BMI=28.4 (IQR,24.9-32.9) Kg/m² and 51.9% with diabetes] were included. A total of 429 individuals [27.0% (95%CI,24.8-29.2)] died during hospitalization (median time 14 (IQR,9-24) days). Older age [vs<40 years; age=60-69 years-aHR=1.89 (95%CI,1.08-3.32); age=70-79 years-aHR=2.52 (95%CI,1.42-4.45); age≥80-aHR=2.90 (95%CI 1.54-5.47)]; noninvasive or mechanical ventilation at admission [vs facial-mask or none; aHR=1.69 (95%CI 1.30-2.19)]; SAPS-III score≥57 [vs<57; aHR=1.47 (95%CI 1.13-1.92)] and SOFA score≥10 [vs <10; aHR=1.51 (95%CI 1.08-2.10)] were independently associated with in-hospital mortality. A total of 65 individuals [6.7% (95%CI 5.3-8.4)] had a rehospitalization or death [rate=323 (95%CI 250-417) per 1000 person-years] in a median time of 52 (range 1-280) days post-hospital discharge. Age ≥ 60 years [vs <60, aHR=2.13 (95%CI 1.15-3.94)] and SAPS-III ≥57 at admission [vs <57, aHR=2.37 (95%CI 1.22-4.59)] were independently associated with rehospitalization or death after hospital discharge. Interpretation: High in-hospital mortality rates due to COVID-19 were observed and elderly people remained at high risk of rehospitalization and death after hospital discharge. Funding: Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Programa INOVA-FIOCRUZ.

SARS-CoV-2 testing disparities across geographical regions from a large metropolitan area in Brazil: Results from a web-based survey among individuals interested in clinical trials for COVID-19 vaccines.

After more than a year since the novel coronavirus (SARS-CoV-2) disease 2019 or COVID-19 has reached the status of a global pandemic, the number of COVID-19 cases continues to rise in Brazil. As no effective treatment been approved yet, only mass vaccination can stop the spread of SARS-CoV-2 and end the COVID-19 pandemic. Multiple COVID-19 vaccine candidates are under development and some are currently in use. This study aims to describe the characteristics of individuals who have registered in an online platform to participate in clinical trials for COVID-19 vaccines. Additionally, participants' characteristics according to age and presence of comorbidities associated with severe COVID-19 and differences of SARS-CoV-2 testing across different geographical areas/neighborhoods are provided. This was a cross-sectional web-based study conducted between September and December/2020, aiming to reach individuals aged ≥18 years who live in Rio de Janeiro metropolitan area, Brazil. Among 21,210 individuals who completed the survey, 20,587 (97.1%) were willing to participate in clinical trials for COVID-19 vaccines. Among those willing to participate, 57.8% individuals were aged 18-59 years and had no comorbidity, 33.7% were aged 18-59 years and had at least one comorbidity, and 8.6% were aged ≥ 60 years regardless the presence of any comorbidity. Almost half (42.6%) reported ever testing for COVID-19, and this proportion was lower among those aged ≥ 60 years (p < 0.001). Prevalence of positive PCR results was 16.0%, higher among those aged 18-59 years (p < 0.009). Prevalence of positive antibody result was 10.0%, with no difference across age and comorbidity groups. Participants from areas/neighborhoods with higher Human Development Index (HDI) reported ever testing for SARS-CoV-2 more frequently than those from lower HDI areas. Interest to participate in clinical trials for COVID-19 vaccines candidates in Rio de Janeiro was significantly high. The online registry successfully reached out a large number of individuals with diverse sociodemographic, economic and clinical backgrounds.

A randomized double-blind controlled trial of convalescent plasma in adults with severe COVID-19.

BACKGROUNDAlthough convalescent plasma has been widely used to treat severe coronavirus disease 2019 (COVID-19), data from randomized controlled trials that support its efficacy are limited.METHODSWe conducted a randomized, double-blind, controlled trial among adults hospitalized with severe and critical COVID-19 at 5 sites in New York City (USA) and Rio de Janeiro (Brazil). Patients were randomized 2:1 to receive a single transfusion of either convalescent plasma or normal control plasma. The primary outcome was clinical status at 28 days following randomization, measured using an ordinal scale and analyzed using a proportional odds model in the intention-to-treat population.RESULTSOf 223 participants enrolled, 150 were randomized to receive convalescent plasma and 73 to receive normal control plasma. At 28 days, no significant improvement in the clinical scale was observed in participants randomized to convalescent plasma (OR 1.50, 95% confidence interval [CI] 0.83-2.68, P = 0.180). However, 28-day mortality was significantly lower in participants randomized to convalescent plasma versus control plasma (19/150 [12.6%] versus 18/73 [24.6%], OR 0.44, 95% CI 0.22-0.91, P = 0.034). The median titer of anti-SARS-CoV-2 neutralizing antibody in infused convalescent plasma units was 1:160 (IQR 1:80-1:320). In a subset of nasopharyngeal swab samples from Brazil that underwent genomic sequencing, no evidence of neutralization-escape mutants was detected.CONCLUSIONIn adults hospitalized with severe COVID-19, use of convalescent plasma was not associated with significant improvement in day 28 clinical status. However, convalescent plasma was associated with significantly improved survival. A possible explanation is that survivors remained hospitalized at their baseline clinical status.TRIAL REGISTRATIONClinicalTrials.gov, NCT04359810.FUNDINGAmazon Foundation, Skoll Foundation.

High acceptability of PrEP teleconsultation and HIV self-testing among PrEP users during the COVID-19 pandemic in Brazil.

In March 2020, telemedicine and HIV self-testing were adopted by Brazilian Public Health services to minimize disruptions in pre-exposure prophylaxis (PrEP) access and delivery during the COVID-19 pandemic. To understand the acceptability of PrEP teleconsultation and HIV self-testing, we conducted a web-based study during social distancing period (April-May, 2020) among men who have sex with men and transgender/non-binary individuals using social media. Out of the 2375 HIV negative respondents, 680 reported PrEP use and were included in this analysis. Median age was 33 years (IQR: 28-40), 98% cisgender men, 56% white, 74% high education, and 68% middle/high income. Willingness to use HIVST was 79% and 32% received an HIV self-testing during social distancing period. The majority reported preference for PrEP/HIV self-testing home delivery instead of collecting at the service. PrEP teleconsultation was experienced by 21% and most reported feeling satisfied with the procedures. High acceptability of PrEP teleconsultation was reported by 70%. In ordinal logistic model, having higher education was associated with high aceptability of PrEP teleconsultation (aOR:1.62; 95%CI: 1.07-2.45). Our results point out that PrEP teleconsultation and PrEP/HIV self-testing home delivery could be implemented by PrEP services in Brazil to avoid PrEP shortage during the COVID-19 pandemic and thereafter as an option to increase retention and adherence.

Telemedicine as a tool for PrEP delivery during the COVID-19 pandemic in a large HIV prevention service in Rio de Janeiro-Brazil

COVID-19 public health responses such as social distancing and community containment measures protocols are critical to preventing and containing the spread of coronavirus. Brazil accounts for almost half of Latin American HIV cases and Rio de Janeiro is the city with the second largest number of AIDS. Clinical appointments and pharmacy antiretroviral refills may be impaired due to restricted traffic and possible lockdowns, preventing people living with HIV and those using PrEP from accessing needed antiretrovirals. We hereby describe the telemedicine procedures implemented in a large PrEP delivery service in Rio de janeiro in the context of the COVID-19 pandemic. At the initial teleconsultation, individuals undergoe HIV rapid testing and are assessed by phone for PrEP related procedures. Individuals receive a digital prescription to retrieve a 120-day PrEP supply plus two HIV self-test kits. Subsequent follow-up teleconsultations will be performed remotely by phone call, including instructions for the HIV self-test performance, which results are to be sent using a digital picture. Participants will attend the service only for PrEP refill. The use of telemedicine procedures is being effective to avoid PrEP shortage and reduce the time PrEP users spend at the service during the COVID-19 pandemic and social distancing recommendations.

COVID-19: a meta-analysis of diagnostic test accuracy of commercial assays registered in Brazil

ABSTRACT The accuracy of commercially available tests for COVID-19 in Brazil remains unclear. We aimed to perform a meta-analysis to describe the accuracy of available tests to detect COVID-19 in Brazil. We searched at the Brazilian Health Regulatory Agency (ANVISA) online platform to describe the pooled sensitivity (Se), specificity (Sp), diagnostic odds ratio (DOR) and summary receiver operating characteristic curves (SROC) for detection of IgM/IgG antibodies and for tests using naso/oropharyngeal swabs in the random-effects models. We identified 16 tests registered, mostly rapid-tests. Pooled diagnostic accuracy measures [95%CI] were: (i) for IgM antibodies Se = 82% [76-87];Sp = 97% [96-98];DOR = 168 [92-305] and SROC = 0.98 [0.96-0.99];(ii) for IgG antibodies Se = 97% [90-99];Sp = 98% [97-99];DOR = 1994 [385-10334] and SROC = 0.99 [0.98-1.00];and (iii) for detection of SARS-CoV-2 by antigen or molecular assays in naso/oropharyngeal swabs Se = 97% [85-99];Sp = 99% [77-100];DOR = 2649 [30-233056] and SROC = 0.99 [0.98-1.00]. These tests can be helpful for emergency testing during the COVID-19 pandemic in Brazil. However, it is important to highlight the high rate of false negative results from tests which detect SARS-CoV-2 IgM antibodies in the initial course of the disease and the scarce evidence-based validation results published in Brazil. Future studies addressing the diagnostic performance of tests for COVID-19 in the Brazilian population are urgently needed.

Impact of COVID-19 Pandemic on Sexual Minority Populations in Brazil: An Analysis of Social/Racial Disparities in Maintaining Social Distancing and a Description of Sexual Behavior.

We conducted a web-based survey to understand the impact of social distancing measures on Brazilian MSM and transgender/non-binary lives. A total of 3486 respondents were included in this analysis and the great majority were cismen (98%). The median age was 32 years (IQR: 27-40), 44% non-white, 36% low schooling and 38% low income. Most of participants reported HIV negative/unknown status (77%). Participants on-PrEP reported more condomless anal sex than those off-PrEP. Conversely, 24% off-PrEP were at substantial HIV-risk. PrEP/ART continuation were reported by the majority, despite reports of impediments to medication refill. Transgender/non-binary reported more mental health problems and challenges to access health care. Social and racial disparities were associated with unattainability of maintaining social distancing. Tailored social and economic support policies during COVID-19 pandemic should be made available to these populations. Challenges for PrEP/ART access will demand the implementation of innovative solutions to avoid the expansion of the HIV epidemic.

Telemedicine as a tool for PrEP delivery during the COVID-19 pandemic in a large HIV prevention service in Rio de Janeiro-Brazil.

COVID-19 public health responses such as social distancing and community containment measures protocols are critical to preventing and containing the spread of coronavirus. Brazil accounts for almost half of Latin American HIV cases and Rio de Janeiro is the city with the second largest number of AIDS. Clinical appointments and pharmacy antiretroviral refills may be impaired due to restricted traffic and possible lockdowns, preventing people living with HIV and those using PrEP from accessing needed antiretrovirals. We hereby describe the telemedicine procedures implemented in a large PrEP delivery service in Rio de janeiro in the context of the COVID-19 pandemic. At the initial teleconsultation, individuals undergoe HIV rapid testing and are assessed by phone for PrEP related procedures. Individuals receive a digital prescription to retrieve a 120-day PrEP supply plus two HIV self-test kits. Subsequent follow-up teleconsultations will be performed remotely by phone call, including instructions for the HIV self-test performance, which results are to be sent using a digital picture. Participants will attend the service only for PrEP refill. The use of telemedicine procedures is being effective to avoid PrEP shortage and reduce the time PrEP users spend at the service during the COVID-19 pandemic and social distancing recommendations.

COVID-19: a meta-analysis of diagnostic test accuracy of commercial assays registered in Brazil.

The accuracy of commercially available tests for COVID-19 in Brazil remains unclear. We aimed to perform a meta-analysis to describe the accuracy of available tests to detect COVID-19 in Brazil. We searched at the Brazilian Health Regulatory Agency (ANVISA) online platform to describe the pooled sensitivity (Se), specificity (Sp), diagnostic odds ratio (DOR) and summary receiver operating characteristic curves (SROC) for detection of IgM/IgG antibodies and for tests using naso/oropharyngeal swabs in the random-effects models. We identified 16 tests registered, mostly rapid-tests. Pooled diagnostic accuracy measures [95%CI] were: (i) for IgM antibodies Se=82% [76-87]; Sp=97% [96-98]; DOR=168 [92-305] and SROC=0.98 [0.96-0.99]; (ii) for IgG antibodies Se=97% [90-99]; Sp=98% [97-99]; DOR=1994 [385-10334] and SROC=0.99 [0.98-1.00]; and (iii) for detection of SARS-CoV-2 by antigen or molecular assays in naso/oropharyngeal swabs Se=97% [85-99]; Sp=99% [77-100]; DOR=2649 [30-233056] and SROC=0.99 [0.98-1.00]. These tests can be helpful for emergency testing during the COVID-19 pandemic in Brazil. However, it is important to highlight the high rate of false negative results from tests which detect SARS-CoV-2 IgM antibodies in the initial course of the disease and the scarce evidence-based validation results published in Brazil. Future studies addressing the diagnostic performance of tests for COVID-19 in the Brazilian population are urgently needed.