Influence of SARS-CoV-2 variants on COVID-19 epidemiological and clinical profiles: a comparative analysis of two waves of cases.

BACKGROUND: The COVID-19 pandemic has been the most significant health challenge of the last century. Multiple and successive waves of COVID-19 cases, driven particularly by the emergence of new SARS-CoV-2 variants, have kept the world in a constant state of alert. METHODS: We present an observational, descriptive, cross-sectional study aimed at identifying SARS-CoV-2 variants circulating during two local waves of COVID-19 cases in southern Bahia, Brazil (late 2021 and late 2022), and analyzing the association between the detected variants and the epidemiological and clinical characteristics of the disease. For this purpose, data and nasopharyngeal samples from individuals in southern Bahia, Brazil, with suspected COVID-19 were included. Viral detection was performed by RT-qPCR, and SARS-CoV-2 variants were identified by next-generation viral sequencing. RESULTS: A total of 368 nasopharyngeal samples were tested. Approximately 23% of the samples from late 2021 tested positive for SARS-CoV-2, while in 2022, the positivity rate was about 56%. All sequenced samples from 2021 were identified as the Delta variant, while in 2022, all samples were classified as the Omicron variant. Overall, individuals who tested positive for SARS-CoV-2 in 2022 were younger than those who tested positive in 2021. Moreover, we observed significant differences in the clinical spectrum of SARS-CoV-2 infection when comparing the two periods. Individuals who presented with anosmia/ageusia were more likely to test positive for SARS-CoV-2 infection in 2021 but not in 2022. Additionally, fever, dry cough, pharyngalgia, headache, and rhinorrhea were more frequent among individuals infected with the Omicron variant than among those infected with the Delta variant. CONCLUSIONS: The profile of COVID-19 in southern Bahia differed when analyzing two distinct waves of the pandemic in the region. These differences are likely related to the variants, which may differ in transmissibility and virulence, thereby altering the dynamics of the pandemic. This underscores the importance of genomic surveillance in better understanding the behavior of viral infections.

SARS-CoV-2 Infection in Cities from the Southern Region of Bahia State, Brazil: Analysis of Variables Associated in Both Individual and Community Level.

The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), challenged public health systems worldwide. Individuals in low-income countries/regions are still at individual and community risk concerning inequality, sanitation, and economic conditions. Besides, during the pandemic, the transmission in municipalities and communities in the countryside and less developed regions kept viral spread and required structured and strengthened clinical and laboratory surveillance. Here, we present an observational, analytic, cross-sectional study conducted using secondary data from the Laboratório de Farmacogenômica e Epidemiologia Molecular (LAFEM)-Universidade Estadual de Santa Cruz (UESC), to evaluate individual and community factors associated to SARS-CoV-2 infection in outpatients from different cities from Southern Region of Bahia State, in Brazil. The data were collected between June 2021 and May 2022. The SARS-CoV-2 positivity by RT-qPCR was correlated with low socio-economic indicators, including the Human development index (HDIc) and Average worker salary (AWSc). Besides, in general, females were less likely to test positive for SARS-CoV-2 (OR = 0.752; CI 95% 0.663-0.853; p < 0.0001), while brown individuals had more positivity for infection (p < 0.0001). In addition, those who had clinical symptoms were more likely to test positive for SARS-CoV-2 (OR = 6.000; CI 95% 4.932-7.299; p < 0.0001). Although dry cough, headache, and fever were the most frequent, loss of taste (OR = 5.574; CI 95% 4.334-7.186) and loss of smell (OR = 6.327; CI 95% 4.899-8.144) presented higher odds ratio to be positive to SARS-CoV-2 by RT-qPCR. Nonetheless, the distribution of these characteristics was not homogenous among the different cities, especially for age and gender. The dynamic of SARS-CoV-2 positivity differed between cities and the total population and reinforces the hypothesis that control strategies for prevention needed to be developed based on both individual and community risk levels to mitigate harm to individuals and the health system.

Ex-vivo mucolytic and anti-inflammatory activity of BromAc in tracheal aspirates from COVID-19.

COVID-19 is a lethal disease caused by the pandemic SARS-CoV-2, which continues to be a public health threat. COVID-19 is principally a respiratory disease and is often associated with sputum retention and cytokine storm, for which there are limited therapeutic options. In this regard, we evaluated the use of BromAc®, a combination of Bromelain and Acetylcysteine (NAC). Both drugs present mucolytic effect and have been studied to treat COVID-19. Therefore, we sought to examine the mucolytic and anti-inflammatory effect of BromAc® in tracheal aspirate samples from critically ill COVID-19 patients requiring mechanical ventilation. METHOD: Tracheal aspirate samples from COVID-19 patients were collected following next of kin consent and mucolysis, rheometry and cytokine analysis using Luminex kit was performed. RESULTS: BromAc® displayed a robust mucolytic effect in a dose dependent manner on COVID-19 sputum ex vivo. BromAc® showed anti-inflammatory activity, reducing the action of cytokine storm, chemokines including MIP-1alpha, CXCL8, MIP-1b, MCP-1 and IP-10, and regulatory cytokines IL-5, IL-10, IL-13 IL-1Ra and total reduction for IL-9 compared to NAC alone and control. BromAc® acted on IL-6, demonstrating a reduction in G-CSF and VEGF-D at concentrations of 125 and 250 µg. CONCLUSION: These results indicate robust mucolytic and anti-inflammatory effect of BromAc® ex vivo in tracheal aspirates from critically ill COVID-19 patients, indicating its potential to be further assessed as pharmacological treatment for COVID-19.

Characteristics and Factors Associated with SARS-CoV-2 Infections in Individuals That Attended Referral Hospitals from Southern Region of Bahia State, Brazil: A Surveillance Network Retrospective Study.

In December 2019, a novel coronavirus was detected in Wuhan, China, and rapidly spread worldwide. In Brazil, to date, there have been more than 20,000,000 confirmed cases of COVID-19 and more than 550,000 deaths. The purpose of the current study was to determine the clinical and epidemiological profile of the population affected by COVID-19 that have attended referral hospitals in Southern region of Bahia State, to better understand the disease and its risk factors in order to enable more appropriate conduct for patients. An observational, descriptive, cross-sectional, exploratory study was conducted using secondary data collected from the Laboratório de Farmacogenômica e Epidemiologia Molecular, Universidade Estadual de Santa Cruz (LAFEM/UESC). Chi-squared and Fisher's exact tests were applied to determine the association between clinical symptoms and laboratory results, and to identify risk factors associated with SARS-CoV-2 infection. A total of 3135 individuals with suspected severe respiratory illness were analyzed and 41.4% of them tested positive for SARS-CoV-2 infection. Male individuals and having comorbidities were risk factors significantly associated with SARS-CoV-2 infection (OR = 1.17 and OR = 1.37, respectively). Interestingly, being a healthcare professional was a significantly protective factor (OR = 0.81, p < 0.001). Our findings highlight the importance of routinely testing the population for early identification of infected individuals, and also provide important information to health authorities and police makers to improve control measures, management, and screening protocols.

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil.

The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The novel viral lineages P.1 (Variant of Concern Gamma) and P.2, respectively identified in the Brazilian states of Amazonas and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed the whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraíba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) in order to monitor the spread of SARS-CoV-2 lineages in Brazil in the first months of 2021. Here, we showed a widespread dispersal of P.1 and P.2 across Brazilian regions and, except for Amazonas, P.2 was the predominant lineage identified in the sampled states. We estimated the origin of P.2 lineage to have happened in February, 2020 and identified that it has differentiated into new clades. Interstate transmission of P.2 was detected since March, but reached its peak in December, 2020 and January, 2021. Transmission of P.1 was also high in December and its origin was inferred to have happened in August 2020. We also confirmed the presence of lineage P.7, recently described in the southernmost region of Brazil, to have spread across the Northeastern states. P.1, P.2 and P.7 are descended from the ancient B.1.1.28 strain, which co-dominated the first phase of the pandemic in Brazil with the B.1.1.33 strain. We also identified the occurrence of a new lineage descending from B.1.1.33 that convergently carries the E484K mutation, N.9. Indeed, the recurrent report of many novel SARS-CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing of the SARS-CoV-2 isolates worldwide in order to identify novel variants of interest and monitor for vaccine effectiveness.

First genome sequencing of SARS-CoV-2 recovered from an infected cat and its owner in Latin America.

An 11-year-old male mixed-breed cat, with exclusively indoor life, presented 3 cough episodes after the owners tested positive by RT-PCR for SARS-CoV-2. The house is inhabited by 5 people (3 adults and 2 children), and 2 of the adults have shown mild symptoms associated with throat discomfort. The cat was vaccinated, had no history of any previous disease, and tested negative for feline coronavirus (FCoV), feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV). Rectal sample collected from the cat was positive for SARS-CoV-2 by RT-PCR. Viral genome sequences recovered from human and cat samples showed an average 99.4% sequence identity. This is the first report of genome sequences of SARS-CoV-2 recovered from a cat and its owner in Latin America.

Frequency and factors associated with Toxoplasma gondii infection in pregnant women and their pets in Ilhéus, Bahia, Brazil.

INTRODUCTION: Toxoplasmosis is an asymptomatic disease that can lead to systemic disease in the fetus of pregnant women with primary infection. This study aimed to determine the prevalence of toxoplasmosis, associated factors, and correlation between the serology of pregnant women and their pets, in the municipality of Ilhéus, Bahia, Brazil. METHODS: This cross-sectional study was conducted in 196 pregnant women and their cats or dogs (n=89). Semi-structured interviews were conducted and serum samples from the pregnant women were tested to detect IgM and IgG antibodies against Toxoplasma gondii, and avidity tests were performed for IgM-positive samples. The serum collected from pets were tested for IgG antibodies, and IgM antibodies in cats. A non-conditional logistic regression analysis was performed to identify infection-associated factors. RESULTS: IgG and IgM antibodies were detected in 67.9% (133/196) and 1.5% (3/196) samples, respectively, for women with an avidity of over 60%. Age ≥ 25 and the presence of cats in the vicinity were found to be associated with infection, while the level of education and previous orientation toward prevention of toxoplasmosis were protective factors in pregnant women. IgG antibodies were detected in 46.1% (41/89) of the animals, and cats were found to be negative for IgM. For the animals, age ≥ 1 year was a factor associated with infection. There was no correlation between serology of the pregnant women and the animals (p=0.15). CONCLUSIONS: An elevated prevalence of toxoplasmosis was detected in the region. Therefore, the adoption of preventive measures by public healthcare bodies is recommended.

Frequency and factors associated with Toxoplasma gondii infection in pregnant women and their pets in Ilhéus, Bahia, Brazil

Abstract INTRODUCTION: Toxoplasmosis is an asymptomatic disease that can lead to systemic disease in the fetus of pregnant women with primary infection. This study aimed to determine the prevalence of toxoplasmosis, associated factors, and correlation between the serology of pregnant women and their pets, in the municipality of Ilhéus, Bahia, Brazil. METHODS: This cross-sectional study was conducted in 196 pregnant women and their cats or dogs (n=89). Semi-structured interviews were conducted and serum samples from the pregnant women were tested to detect IgM and IgG antibodies against Toxoplasma gondii, and avidity tests were performed for IgM-positive samples. The serum collected from pets were tested for IgG antibodies, and IgM antibodies in cats. A non-conditional logistic regression analysis was performed to identify infection-associated factors. RESULTS: IgG and IgM antibodies were detected in 67.9% (133/196) and 1.5% (3/196) samples, respectively, for women with an avidity of over 60%. Age ≥ 25 and the presence of cats in the vicinity were found to be associated with infection, while the level of education and previous orientation toward prevention of toxoplasmosis were protective factors in pregnant women. IgG antibodies were detected in 46.1% (41/89) of the animals, and cats were found to be negative for IgM. For the animals, age ≥ 1 year was a factor associated with infection. There was no correlation between serology of the pregnant women and the animals (p=0.15). CONCLUSIONS: An elevated prevalence of toxoplasmosis was detected in the region. Therefore, the adoption of preventive measures by public healthcare bodies is recommended.