Cohort profile: follow-up of a household cohort throughout five epidemic waves of SARS-CoV-2 in Rio de Janeiro, Brazil.

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.

Cohort profile: follow-up of a household cohort throughout five epidemic waves of SARS-CoV-2 in Rio de Janeiro, Brazil / Perfil da coorte: acompanhamento de uma coorte domiciliar ao longo de cinco ondas epidêmicas de SARS-CoV-2 no Rio de Janeiro, Brasil / Perfil de la cohorte: seguimiento de una cohorte de hogares durante cinco olas epidémicas de SARS-CoV-2 en Río de Janeiro, Brasil

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.

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.

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.

Predictors of chronic joint pain after Chikungunya virus infection in the INOVACHIK prospective cohort study.

BACKGROUND: Chikungunya can cause persistent chronic joint pain. Knowledge of the risk factors for disease progression is important for preventing and controlling complications. This study aimed to identify factors associated with chronic joint pain. METHODS: This prospective cohort study was conducted at a reference center in Rio de Janeiro. Men and women (aged ≥ 18 years) in the acute phase of Chikungunya were included. Clinical data and samples were collected over three months. Risk factors were evaluated using multivariate and logistic regression analyses. RESULTS: A total of 107 patients were followed up. The incidence rate of joint tenderness was 61.7 %. Female sex (adjusted odds ratio [AOR] 3.24, 95 % confidence interval [CI]:1.07-9.77), diarrhea (AOR 5.08, 95 % CI:1.55-16.67), severe joint pain (AOR 4.26, 95 % CI:1.06-17.06), and CHIKV real-time reverse transcription polymerase chain reaction positivity up to 5 days after the onset of symptoms in urine or saliva (AOR 4.56, 95 % CI:1.41-14.77) were identified as predictors of persistent chronic pain. CONCLUSIONS: In a predominantly female population, musculoskeletal symptoms are not the sole determinant of chronic pain, and careful evaluation of CHIKV detection in alternative body fluids (such as saliva and urine) during the early phase of the disease is warranted.

Long COVID-19 syndrome associated with Omicron XBB.1.5 infection: a case report.

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.

Accuracy of saliva for SARS-CoV-2 detection in outpatients and their household contacts during the circulation of the Omicron variant of concern.

BACKGROUND: While nasopharyngeal (NP) swabs are considered the gold standard for severe acute respiratory coronavirus 2 (SARS-CoV-2) real-time reverse transcriptase-polymerase chain reaction (RT-PCR) detection, several studies have shown that saliva is an alternative specimen for COVID-19 diagnosis and screening. METHODS: To analyze the utility of saliva for the diagnosis of COVID-19 during the circulation of the Omicron variant, participants were enrolled in an ongoing cohort designed to assess the natural history of SARS-CoV-2 infection in adults and children. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Cohen's kappa coefficient were calculated to assess diagnostic performance. RESULTS: Overall, 818 samples were collected from 365 outpatients from January 3 to February 2, 2022. The median age was 32.8 years (range: 3-94 years). RT-PCR for SARS-CoV-2 was confirmed in 97/121 symptomatic patients (80.2%) and 62/244 (25.4%) asymptomatic patients. Substantial agreement between saliva and combined nasopharyngeal/oropharyngeal samples was observed with a Cohen's kappa value of 0.74 [95% confidence interval (CI): 0.67-0.81]. Sensitivity was 77% (95% CI: 70.9-82.2), specificity 95% (95% CI: 91.9-97), PPV 89.8% (95% CI: 83.1-94.4), NPV 87.9% (95% CI: 83.6-91.5), and accuracy 88.5% (95% CI: 85.0-91.4). Sensitivity was higher among samples collected from symptomatic children aged three years and older and adolescents [84% (95% CI: 70.5-92)] with a Cohen's kappa value of 0.63 (95% CI: 0.35-0.91). CONCLUSIONS: Saliva is a reliable fluid for detecting SARS-CoV-2, especially in symptomatic children and adolescents during the circulation of the Omicron variant.

Clinical markers of post-Chikungunya chronic inflammatory joint disease: A Brazilian cohort.

BACKGROUND: Chikungunya-fever (CHIKF) remains a public health major issue. It is clinically divided into three phases: acute, post-acute and chronic. Chronic cases correspond to 25-40% individuals and, though most of them are characterized by long-lasting arthralgia alone, many of them exhibit persistent or recurrent inflammatory signs that define post-Chikungunya chronic inflammatory joint disease (pCHIKV-CIJD). We aimed to identify early clinical markers of evolution to pCHIKV-CIJD during acute and post-acute phases. METHODOLOGY/PRINCIPAL FINDINGS: We studied a prospective cohort of CHIKF-confirmed volunteers with longitudinal clinical data collection from symptoms onset up to 90 days, including a 21-day visit (D21). Of 169 patients with CHIKF, 86 (50.9%) completed the follow-up, from whom 39 met clinical criteria for pCHIKV-CIJD (45.3%). The relative risk of chronification was higher in women compared to men (RR = 1.52; 95% CI = 1.15-1.99; FDR = 0.03). None of the symptoms or signs presented at D0 behaved as an early predictor of pCHIKV-CIJD, while being symptomatic at D21 was a risk factor for chronification (RR = 1.31; 95% CI = 1.09-1.55; FDR = 0.03). Significance was also observed for joint pain (RR = 1.35; 95% CI = 1.12-1.61; FDR = 0.02), reported edema (RR = 3.61; 95% CI = 1.44-9.06; FDR = 0.03), reported hand and/or feet small joints edema (RR = 4.22; 95% CI = 1.51-11.78; FDR = 0.02), and peri-articular edema observed during physical examination (RR = 2.89; 95% CI = 1.58-5.28; FDR = 0.002). Furthermore, patients with no findings in physical examination at D21 were at lower risk of chronic evolution (RR = 0.41, 95% CI = 0.24-0.70, FDR = 0.01). Twenty-nine pCHIKV-CIJD patients had abnormal articular ultrasonography (90.6% of the examined). The most common findings were synovitis (65.5%) and joint effusion (58.6%). CONCLUSION: This cohort has provided important insights into the prognostic evaluation of CHIKF. Symptomatic sub-acute disease is a relevant predictor of evolution to chronic arthritis with synovitis, drawing attention to joint pain, edema, multiple articular involvement including small hand and feet joints as risk factors for chronification beyond three months, especially in women. Future studies are needed to accomplish the identification of accurate and early biomarkers of poor clinical prognosis, which would allow better understanding of the disease's evolution and improve patients' management, modifying CHIKF burden on global public health.

Long COVID-19 syndrome associated with Omicron XBB.1.5 infection: a case report

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.

Chikungunya Virus Shedding in Semen: A Case Series.

BACKGROUND: Chikungunya is a viral disease that is transmitted by mosquitoes. It is characterized by an acute onset of fever and severe arthralgia. METHODS: We describe six cases of acute and post-acute chikungunya in which viral RNA was detected in semen. CONCLUSIONS: The most prolonged detection period was 56 days after illness onset. We attempted to cultivate positive semen samples, but virus isolation was unsuccessful in all cases.

Detection of Chikungunya virus in bodily fluids: The INOVACHIK cohort study.

BACKGROUND: Chikungunya is a widely distributed, re-emerging tropical disease caused by the chikungunya virus (CHIKV). Little is known about the duration for which CHIK RNA are detectable in bodily fluids, especially genital secretions, and current evidence is based on small series or case reports. An understanding of viral dynamics across different body compartments can inform diagnostic testing algorithms and public health prevention interventions. METHODOLOGY: A prospective cohort study was conducted to assess the presence and duration of detectable levels of CHIKV RNA in blood, urine, saliva, semen, and vaginal secretions. Men and women (≥ 18 years) with a positive reverse transcriptase-polymerase chain reaction (RT-PCR) test for CHIKV in the acute phase (1-14 days) of the disease were included. After enrollment, clinical data and samples were collected every 15 days over the first 2 months, and a final collection was performed 3 months after recruitment. The Kaplan-Meier interval-censoring method and the parametric Weibull model were fitted to estimate the median time of viral persistence until the lack of CHIKV RNA detection among all body fluids. Punctual estimates of the median time of CHIKV RNA persistence for each fluid were estimated using a 95% confidence interval (CI). RESULTS: From April to December 2019, 170 participants were screened. Of these, 152 (100 women) were enrolled in the study. The median and interquartile range (IQR) ages for men and women were 39.3 (IQR: 26.9, 50.7) and 43.5 (IQR: 33.8, 53.6) years, respectively. CHIKV RNA was detected in 80.3% (122/152) of serum samples, 23.0% (35/152) of urine samples, 30.3% (46/152) of saliva samples, 14.3% (6/42) of semen samples, and 20.2% (20/99) of vaginal secretion samples. The median time until the loss of CHIKV RNA detection was 19.6 days (95% CI, 17.5-21.7) in serum, 25.3 days (95% CI, 17.8-32.8) in urine, 23.1 days (95% CI, 17.9-28.4) in saliva, and 25.8 days (95% CI, 20.6-31.1) in vaginal secretion. The number of semen samples available was too small to make statistical estimates, but a last positive sample was obtained from a participant 56 days after the onset of symptoms. CONCLUSIONS: CHIKV RNA could be detected in all bodily fluids studied, including genital secretions during the acute and convalescent phases and additional studies on viral infectivity in semen and vaginal secretions are warranted.

Post-acute COVID-19 syndrome after reinfection and vaccine breakthrough by the SARS-CoV-2 Gamma variant in Brazil.

We describe a case of prolonged COVID-19 caused by the SARS-CoV-2 Gamma variant in a fully vaccinated healthcare worker, 387 days after an infection caused by lineage B.1.1.33. Infections were confirmed by whole-genome sequencing and corroborated by the detection of neutralizing antibodies in convalescent serum samples. Considering the permanent exposure of this healthcare worker to SARS-CoV-2, the waning immunity after the first infection, the low efficacy of the inactivated vaccine at preventing COVID-19, the immune escape of the Gamma variant (VOC), and the burden of post-COVID syndrome, this individual would have benefited from an additional dose of a heterologous vaccine.

Investigation of SARS-CoV-2 infection in dogs and cats of humans diagnosed with COVID-19 in Rio de Janeiro, Brazil.

BACKGROUND: Infection by SARS-CoV-2 in domestic animals has been related to close contact with humans diagnosed with COVID-19. Objectives: To assess the exposure, infection, and persistence by SARS-CoV-2 of dogs and cats living in the same households of humans that tested positive for SARS-CoV-2, and to investigate clinical and laboratory alterations associated with animal infection. METHODS: Animals living with COVID-19 patients were longitudinally followed and had nasopharyngeal/oropharyngeal and rectal swabs collected and tested for SARS-CoV-2. Additionally, blood samples were collected for laboratory analysis, and plaque reduction neutralization test (PRNT90) to investigate specific SARS-CoV-2 antibodies. RESULTS: Between May and October 2020, 39 pets (29 dogs and 10 cats) of 21 patients were investigated. Nine dogs (31%) and four cats (40%) from 10 (47.6%) households were infected with or seropositive for SARS-CoV-2. Animals tested positive from 11 to 51 days after the human index COVID-19 case onset of symptoms. Three dogs tested positive twice within 14, 30, and 31 days apart. SARS-CoV-2 neutralizing antibodies were detected in one dog (3.4%) and two cats (20%). In this study, six out of thirteen animals either infected with or seropositive for SARS-CoV-2 have developed mild but reversible signs of the disease. Using logistic regression analysis, neutering, and sharing bed with the ill owner were associated with pet infection. CONCLUSIONS: The presence and persistence of SARS-CoV-2 infection have been identified in dogs and cats from households with human COVID-19 cases in Rio de Janeiro, Brazil. People with COVID-19 should avoid close contact with their pets during the time of their illness.

Characterization of aneuploidy in interspecific hybrid between Urochloa ruziziensis (R. Germ. & Evrard) Crins and Urochloa decumbens (Stapf) R. D. Webster.

The aim of the study was to characterize the type of aneuploidy present in the hybrid Urochloa ruziziensis × Urochloa decumbens and to confirm the origin of the additional chromosomes through comparative analysis of the hybrid and parental karyotypes. C and CMA banding techniques were used for chromosome differentiation. The parental genotypes showed 36 chromosomes. The hybrid presented plants with 36 + 2 chromosomes and plants with 36 + 1 chromosomes. Urochloa ruziziensis (4x) presented four chromosomes with CMA and C bands co-located in the terminal position. In U. decumbens, four chromosomes presented terminal CMA bands, eight chromosomes were distinguished by C banding with pericentromeric and terminal bands, one chromosome with terminal band at both ends and one chromosome presented one C terminal band. For the hybrid, CMA bands were found on five chromosomes and C bands on seven chromosomes, all in terminal position. Aneuploidy was identified in pairs 3' and 4' in the hybrid plants with 36 + 2 chromosomes, characterizing it as double trisomy. The karyotype of hybrid plants with 36 + 1 chromosomes indicated elimination of the additional chromosome identified in pair 4' and maintenance of trisomy on pair 3'. The comparative analysis of karyotypes indicates that the additional chromosomes that characterize the trisomy were inherited from U. ruziziensis (artificial tetraploid).

Reliability of plant root comet assay in comparison with human leukocyte comet assay for assessment environmental genotoxic agents.

Comet assay is an efficient test to detect genotoxic compounds based on observation of DNA damage. The aim of this work was to compare the results obtained from the comet assay in two different type of cells extracted from the root tips from Lactuca sativa L. and human blood. For this, Spent Pot Liner (SPL), and its components (aluminum and fluoride) were applied as toxic agents. SPL is a solid waste generated in industry from the aluminum mining and processing with known toxicity. Three concentrations of all tested solutions were applied and the damages observed were compared to negative and positive controls. It was observed an increase in the frequency of DNA damage for human leukocytes and plant cells, in all treatments. On human leukocytes, SPL induced the highest percentage of damage, with an average of 87.68%. For root tips cells of L. sativa the highest percentage of damage was detected for aluminum (93.89%). Considering the arbitrary units (AU), the average of nuclei with high levels of DNA fragmentation was significant for both cells type evaluated. The tested cells demonstrated equal effectiveness for detection of the genotoxicity induced by the SPL and its chemical components, aluminum and fluoride. Further, using a unique method, the comet assay, we proved that cells from root tips of Lactuca sativa represent a reliable model to detect DNA damage induced by genotoxic pollutants is in agreement of those observed in human leukocytes as model. So far, plant cells may be suggested as important system to assess the toxicological risk of environmental agents.