Lessons from the COVID-19 pandemic: the unequal burden of COVID-19 on vulnerable populations in the Brazilian Central-West.

This study aimed to estimate the prevalence and identify social factors and preventive strategies associated with the coronavirus disease 2019 (COVID-19) in socio and economically vulnerable people (recyclable waste pikers, immigrants/refugees, and homeless people) in Goiânia, Goiás State, Central-Western Brazil. A cross-sectional study was conducted from July 2020 to October 2020. COVID-19 positivity was defined as a positive total anti-SARS-COV-2 antibody test and/or RNA test for SARS-COV-2. Univariable and multiple regression analyses were performed to identify the variables associated with COVID-19. Of the 594 participants, 47.3% were recyclable waste pickers, 29.6% were immigrants/refugees, and 23.1% were homeless people. The positivity for SARS-CoV-2 RNA was 14.1%, whereas for anti-SARS-CoV-2 a total of 30.8% were positive, and 39.4% were positive for at least one COVID-19 marker. Among the 541 individuals, being immigrants/refugees, not wearing a surgical mask, and having three or more people sleeping in the same room were associated with SARS-CoV-2 infection, while using TV news as the main source of information about the pandemic was a protective predictor of COVID-19. This study revealed ethnic and socioeconomic inequalities in the prevalence of COVID-19 among impoverished people in Brazil. Additionally, a high prevalence of COVID-19 was detected in all three groups. Developing new strategies to combat and prevent communicable diseases affecting this population is essential for mitigating future and ongoing pandemics.

High silent prevalence of human herpesvirus 1 (HSV-1) infection affecting the indigenous reservation of the municipality of Dourados, Central-West Brazil.

BACKGROUND: The indigenous population located in the central region of Brazil, is the second largest in terms of population size in the country. The Indigenous Reserve of Dourados has risk factors that increase the vulnerability of the indigenous population to infectious diseases, especially Human alphaherpesvirus (HSV-1), a neglected disease with high prevalence in priority populations in developing countries. The virus can also cause many more severe diseases, including widespread neonatal infections, herpetic keratitis, and herpes encephalitis, which can be fatal if left untreated. We estimated the prevalence of anti-HSV-1 antibodies and correlated it with the demographic and behavioral characteristics of the Indigenous population of the Jaguapirú and Bororó villages (Dourados, Mato Grosso do Sul (MS), Brazil). METHODS: Our approach was cross-sectional. From March 2017 to November 2018. Using anti-HSV-1 (Gg1) IgM and anti-HSV-1 (gG1) IgG Euroimmun and the detection and quantification of HSV-1 viral load in plasma samples, through real-time PCR. The maps were constructed using QGIS and the statistical analyses using R Studio software. RESULTS: A total of 1138 individuals (> 18 years old) were enrolled. The prevalence of anti-HSV-1 IgM and IgG were 20% and 97.5%, respectively. The prevalence of anti-HSV-1 antibodies for IgG was higher in both sexes. Anti-HSV-1 IgM antibodies were present in 17.1%, 21.2%, 12.5%, and 22% of the participants with urinary problems, genital wounds, genital warts, and urethral discharge, respectively. Real-time PCR was used for confirmatory testing; HSV-1 DNA was detected in 25.6% (54/211) of anti-HSV1 IgM-positive samples. Viral loads ranged from 5.99E + 02 to 3.36E + 13. CONCLUSIONS: The seroprevalence of HSV-1 IgM and detection of HSV-1 DNA in the Indigenous population confirmed high silent prevalence. Furthermore, the seroprevalence of HSV-1 in the Indigenous population was higher than that reported in the general adult Brazilian population. Various socioeconomic factors, drug use, and health and sexual behaviors could contribute to the facilitation of HSV-1 transmission in the Indigenous population. Our results may help develop culturally appropriate intervention programs that eliminate health access barriers and improve the implementation of public health policies aimed at promoting information regarding the prevention, treatment, and control of HSV-1 infection in Brazilian Indigenous populations.

Liver and Inflammatory Biomarkers Are Related to High Mortality in Hospitalized Patients with COVID-19 in Brazilian Amazon Region.

COVID-19 is a multisystem disease with many clinical manifestations, including liver damage and inflammation. The objective of this study is to analyze inflammation biomarkers in relation to the clinical outcome and respiratory symptoms of COVID-19. This is a retrospective cohort of patients with COVID-19 admitted to the Hospital Regional do Baixo Amazonas from 2020 to 2022. Data were collected from electronic medical records from admission to the 30th day of hospitalization and soon after hospital discharge. A total of 397 patients were included in the study. In the longitudinal follow-up of liver markers, a significant difference was found for AST on day 14, with a higher median in the death group. Among the hematological markers, lymphopenia was observed throughout the follow-up, with the death group having the most altered values. When comparing the evolution of biomarkers in the Non-Invasive Ventilation (NIV) and Invasive Mechanical Ventilation (IMV) groups, AST showed a significant difference only on day 14 and GGT on day 1, being greater in the IMV group, and indirect bilirubin on day 7 being more altered in the NIV group. In conclusion, death during hospitalization or a more severe form of COVID-19 was related to significant changes in liver and inflammatory biomarkers.

Genetic variability of hepatitis B virus in acute and in different phases of chronic infection in Brazil.

The selection pressure imposed by the host immune system impacts on hepatitis B virus (HBV) variability. This study evaluates HBV genetic diversity, nucleos(t)ide analogs resistance and HBsAg escape mutations in HBV patients under distinct selective pressures. One hundred and thirteen individuals in different phases of HBV infection were included: 13 HBeAg-positive chronic infection, 9 HBeAg-positive chronic hepatitis, 47 HBeAg-negative chronic infection (ENI), 29 HBeAg-negative chronic hepatitis (ENH) and 15 acute infected individuals. Samples were PCR amplified, sequenced and genetically analyzed for the overlapping POL/S genes. Most HBV carriers presented genotype A (84/113; 74.3%), subgenotype A1 (67/84; 79.7%), irrespective of group, followed by genotypes D (20/113; 17.7%), F (8/113; 7.1%) and E (1/113; 0.9%). Clinically relevant mutations in polymerase (tL180M/M204V) and in the Major Hydrophilic Region of HBsAg (sY100C, T118A/M, sM133T, sD144A and sG145R) were observed. Our findings, however, indicated that most polymorphic sites were located in the cytosolic loops (CYL1-2) and transmembrane domain 4 (TMD4) of HBsAg. Lower viral loads and higher HBV genetic diversity were observed in ENI and ENH groups (p < 0.001), suggesting that these groups are subjected to a higher selective pressure. Our results provide information on the molecular characteristics of HBV in a diverse clinical setting, and may guide future studies on the balance of HBV quasispecies at different stages of infection.

Seroprevalence of anti-SARS-CoV-2 in patients with hepatitis B and C: a pre-vaccination study.

The serological markers for the diagnosis of COVID-19 plays an important role in the epidemiological investigation of the pandemic. This study aims to assess the prevalence of anti-SARS-CoV-2 in hepatitis B and C patients in a pre-vaccination of COVID-19 period. Between March 2020 and January 2021, 199 serum samples from individuals with HBsAg/HBV DNA or anti-HCV/HCV RNA positivity were tested for antibodies (IgM and IgG) against SARS-CoV-2 using Electrochemiluminescent Immunoassay (ECLIA). Among these, 50.3 % (100/199) tested positive for hepatitis C virus infection and 49.7 % (99/199) for hepatitis B virus, confirmed through molecular and serological diagnosis. The anti-SARS-CoV-2 seroprevalence was 24.1 % (48/199) in this population, with 23.23 % (23/99) hepatitis B and 25 % (25/100) hepatitis C patients tested positive for anti-SARS-CoV-2. The higher seroprevalence of anti-SARS-CoV-2 (16.58 %, 33/199) was detected among those over-40 years of age and the month of November 2020 had the highest number of detections 9 % (18/199) with the majority living in impoverished and neglected neighborhoods in the city of Rio de Janeiro. We found a high prevalence of anti-SARS-CoV-2 in patients with viral hepatitis before COVID-19 vaccination. This demonstrates the high exposure of this population during the period of social isolation.

SARS-CoV-2 and dialysis: humoral response, clinical and laboratory impacts before vaccination.

BACKGROUND: Patients with kidney disease on Hemodialysis (HD) are susceptible to Coronavirus Disease (COVID-19) due to multiple risk factors. AIM: This study aims to report the prevalence of antibodies against SARS-CoV-2 among patients on hemodialysis before vaccination in Brazil and to compare with clinical, demographic, and laboratory data. METHODS: Blood samples from 398 Chronic Kidney Disease (CKD) patients treated in three different private institutions in Rio de Janeiro State, Brazil were submitted to the total anti-SARS-CoV-2 testing. Kidney, liver, and hematological markers were also determined. Respiratory samples were tested by real-time PCR for SARS-CoV-2 RNA and positive samples were subjected to high-throughput sequencing on the MinION device. RESULTS: Overall, anti-SARS-CoV-2 prevalence was 54.5 % (217/398) and two individuals had SARS-CoV-2 RNA with variant B.1.1. High anti-SARS-CoV-2 seroprevalence was found in male gender and those with hospital admission in the last 3-months before the inclusion in the study. Lower red blood cell count was observed in the anti-SARS-CoV-2 seropositive group. High levels of anti-SARS-CoV-2 were found in those who reported symptoms, had low levels of eosinophils and low hematocrit, and who practiced physical activity. CONCLUSION: High prevalence of anti-SARS-CoV-2 was found in CKD patients before the universal immunization in Brazil suggesting that dialysis patients were highly exposed to SARS-CoV-2.

Seroprevalence of hepatitis B, C, and D and associated factors in the semi-isolated Yanomami Amazonian indigenous community.

BACKGROUND: Viral hepatitis is a significant health concern among indigenous population in the Americas. In Brazil, reports find high endemicity of HBV and HDV infections has been reported in several indigenous groups. However, few studies have documented the prevalence of HBV, HCV and HDV in the Yanomami. In this study, the prevalence of hepatitis B, C, and D serological markers and potential risk factors were investigated to provide guidance for the development of strategies aimed at reducing viral transmission in the Yanomami indigenous villages. METHODS: This cross-sectional study was carried out in March 2015 and included 430 individuals from four Yanomami villages: Alapusi (n = 78), Castanha/Ahima (n = 126), Gasolina (n = 105), and Taibrapa (n = 121). A rapid test was used for detection of HBsAg and anti-HCV and chemiluminescent immunoassay for anti-HBs, anti-HBc, and anti-HDV antibodies. RESULTS: HBsAg, anti-HBc, and anti-HBs were detected in 8.8, 45.5, and 49.4% of the participants, respectively. The estimated HBV status: current infection 9.6% (38/395); resolved infection 43.3% (171/395); vaccine immunity 20.5% (81/395), and susceptible to HBV 26.6% (105/395). Gasolina presented the lowest prevalence of HBV infection (6.5%) and the highest prevalence of vaccine immunity (26.9%). Children < 15 years old were highly susceptible to infection, as 53.1% did not have antibodies to HBV, while more than 80% of individuals over 45 years of age had been exposed to HBV. The markers for HDV were founded among 12.5% (4/32) of the HBsAg carriers. Anti-HCV was identified in all villages, with the highest prevalence in Alapusi (5.1%). Possible risk factors such as the use of piercings, tattoos, and contact with prospectors showed no statistical difference between the groups. CONCLUSIONS: Viral hepatitis B and serological markers for HCV and HDV were found to be widely distributed among the Yanomami indigenous community, while the prevalence of vaccine immunity to HBV was low. This finding reinforces the importance of promoting systematized diagnostic and vaccination strategies in indigenous communities. Our data confirm that isolated and difficult-to-reach indigenous communities lack appropriate access to diagnosis, treatment, and vaccination.

Could Herpesviridae be the cause of severe acute hepatitis of unknown origin in children?

INTRODUCTION: Severe acute hepatitis (SAH) is defined by a severe inflammation of hepatocytes in the liver parenchyma which can lead to an acute liver failure, a clinical condition with high mortality rate that can be triggered by several factors but is usually associated to hepatotropic viruses' infection. In 2022, cases of children with severe acute hepatitis of unknown origin hospitalized in Glasgow, Scotland, were reported. Possible causes of this condition include, but are not limited to, undiagnosed viral (and non-viral) infections, autoimmune hepatitis, drug and/or chemical toxicity, mitochondrial chain respiratory and metabolic disorders. AREAS COVERED: Herpesviruses can cause severe acute hepatitis, but little is known about the role and the mechanisms of herpesviruses as a causative agent of this type of hepatitis. We review the role of herpesviruses as causative agent of SAH in children and other possible mechanisms involved in this disease. EXPERT OPINION: Differential diagnosis for herpesvirus in SAH should be implemented in all settings. Alternative fluids, such as saliva and dried blood, could be used in the diagnosis to overwhelm the availability of biological specimens at sufficient volume. In the future, genetic studies could also be added to increase the knowledge about severe acute hepatitis in children.

Seroprevalence of anti-SARS-CoV-2 in patients with hepatitis B and C: a pre-vaccination study

Abstract The serological markers for the diagnosis of COVID-19 plays an important role in the epidemiological investigation of the pandemic. This study aims to assess the prevalence of anti-SARS-CoV-2 in hepatitis B and C patients in a pre-vaccination of COVID-19 period. Between March 2020 and January 2021, 199 serum samples from individuals with HBsAg/HBV DNA or anti-HCV/HCV RNA positivity were tested for antibodies (IgM and IgG) against SARS-CoV-2 using Electrochemiluminescent Immunoassay (ECLIA). Among these, 50.3 % (100/199) tested positive for hepatitis C virus infection and 49.7 % (99/199) for hepatitis B virus, confirmed through molecular and serological diagnosis. The anti-SARS-CoV-2 seroprevalence was 24.1 % (48/199) in this population, with 23.23 % (23/99) hepatitis B and 25 % (25/100) hepatitis C patients tested positive for anti-SARS-CoV-2. The higher seroprevalence of anti-SARS-CoV-2 (16.58 %, 33/199) was detected among those over-40 years of age and the month of November 2020 had the highest number of detections 9 % (18/199) with the majority living in impoverished and neglected neighborhoods in the city of Rio de Janeiro. We found a high prevalence of anti-SARS-CoV-2 in patients with viral hepatitis before COVID-19 vaccination. This demonstrates the high exposure of this population during the period of social isolation.

SARS-CoV-2 and dialysis: humoral response, clinical and laboratory impacts before vaccination

Abstract Background Patients with kidney disease on Hemodialysis (HD) are susceptible to Coronavirus Disease (COVID-19) due to multiple risk factors. Aim This study aims to report the prevalence of antibodies against SARS-CoV-2 among patients on hemodialysis before vaccination in Brazil and to compare with clinical, demographic, and laboratory data. Methods Blood samples from 398 Chronic Kidney Disease (CKD) patients treated in three different private institutions in Rio de Janeiro State, Brazil were submitted to the total anti-SARS-CoV-2 testing. Kidney, liver, and hematological markers were also determined. Respiratory samples were tested by real-time PCR for SARS-CoV-2 RNA and positive samples were subjected to high-throughput sequencing on the MinION device. Results Overall, anti-SARS-CoV-2 prevalence was 54.5 % (217/398) and two individuals had SARS-CoV-2 RNA with variant B.1.1. High anti-SARS-CoV-2 seroprevalence was found in male gender and those with hospital admission in the last 3-months before the inclusion in the study. Lower red blood cell count was observed in the anti-SARS-CoV-2 seropositive group. High levels of anti-SARS-CoV-2 were found in those who reported symptoms, had low levels of eosinophils and low hematocrit, and who practiced physical activity. Conclusion High prevalence of anti-SARS-CoV-2 was found in CKD patients before the universal immunization in Brazil suggesting that dialysis patients were highly exposed to SARS-CoV-2.

Hepatitis E Prevalence in Vulnerable Populations in Goiânia, Central Brazil.

A transversal study was conducted among 472 vulnerable individuals (recyclable waste pickers, immigrants and refugees, homeless individuals, as well as lesbian, gay, bisexual, and transexual individuals) in Goiânia City, the capital of the State of Goiás, Brazil, to investigate the prevalence of hepatitis E virus (HEV) infection. A total of 459 (97.2%) serum samples were tested for anti-HEV IgG and IgM antibodies using fully automated chemiluminescence immunoassays (Liaison® Murex Anti-HEV IgG and IgM assays, DiaSorin, Saluggia, Italy). Positive samples were tested for the presence of HEV RNA by a real-time polymerase chain reaction. A seroprevalence of 0.87% (95% confidence interval [CI]: 0.34-2.22) was found for anti-HEV IgG. Furthermore, anti-HEV IgM was detected in only one individual (0.22%; 95% CI: 0.04-1.22), who was also negative for HEV RNA. These findings revealed that HEV infection is infrequent in vulnerable individuals in Central Brazil, with low seroprevalence of past and recent HEV infections.

Genetic diversity of hepatitis B virus quasispecies in different biological compartments reveals distinct genotypes.

The selection pressure imposed by the host immune system impacts hepatitis B virus (HBV) quasispecies variability. This study evaluates HBV genetic diversity in different biological fluids. Twenty paired serum, oral fluid, and DBS samples from chronic HBV carriers were analyzed using both Sanger and next generation sequencing (NGS). The mean HBV viral load in serum was 5.19 ± 4.3 log IU/mL (median 5.29, IQR 3.01-7.93). Genotype distribution was: HBV/A1 55% (11/20), A2 15% (3/20), D3 10% (2/20), F2 15% (3/20), and F4 5% (1/20). Genotype agreement between serum and oral fluid was 100% (genetic distances 0.0-0.006), while that between serum and DBS was 80% (genetic distances 0.0-0.115). Two individuals presented discordant genotypes in serum and DBS. Minor population analysis revealed a mixed population. All samples displayed mutations in polymerase and/or surface genes. Major population analysis of the polymerase pointed to positions H122 and M129 as the most polymorphic (≥ 75% variability), followed by V163 (55%) and I253 (50%). Neither Sanger nor NGS detected any antiviral primary resistance mutations in the major populations. Minor population analysis, however, demonstrated the rtM204I resistance mutation in all individuals, ranging from 2.8 to 7.5% in serum, 2.5 to 6.3% in oral fluid, and 3.6 to 7.2% in DBS. This study demonstrated that different fluids can be used to assess HBV diversity, nonetheless, genotypic differences according to biological compartments can be observed.

Avian anti-HBV immunoglobulin: New tool to improve hepatitis B diagnosis methods.

Immunoglobulin Y (IgY) could be used in serological diagnosis focused on several infectious agents. This study aims to produce IgY anti-hepatitis B virus surface antigen (anti-HBs) and to assess its use in enzyme immunoassays. Antibodies were produced by immunizing chickens with Hepatitis B vaccine associated (group A), or not, with adjuvant CpG-ODN (group B). Eggs were collected for 20 weeks, yolks were purified based on using polyethylene glycol and affinity chromatography. IgY anti-HBs was featured based on SDS-PAGE and Western Blot techniques. Total protein concentration was measured through spectrophotometry. In-house ELISA used to detect HBsAg was developed based on using IgG/HRP conjugate and IgY-anti-HBs sensitized microplates. Thus, IgY anti-HBs were confirmed through molecular pattern based on SDS-PAGE, whereas specificity of anti-HBs was confirmed through Western Blot. Mean total protein reached 3.27 ± 3.00 mg/mL and 3.11 ± 3.12 mg/mL in groups A and B, respectively. In-house ELISA was developed based on using a panel of HBV positive and negative serum samples; it recorded 100 % sensitivity and 78.9 % specificity to detect HBsAg. In conclusion, it was possible producing anti-HBs IgY by immunizing chickens with HBV vaccine; this molecule could be used as capture antibody to help detecting HBsAg in-house ELISA.

Development of quantitative multiplex RT-qPCR one step assay for detection of hepatitis delta virus.

Hepatitis Delta is a disease caused by exposure to hepatitis B (HBV) and hepatitis D (HDV) viruses, usually with a more severe clinical outcome when compared to an HBV monoinfection. To date, the real prevalence of HDV infection is underestimated and detection methods are poorly available, especially in more endemic regions. Therefore, a one-step RT-qPCR method for quantification of HDV-RNA was developed. Biological samples were selected between 2017 and 2023 from patients at the Ambulatório Especializado em Hepatites Virais of the Centro de Pesquisa em Medicina Tropical de Rondônia and Serviço de Assistência Especializada and underwent the test developed by this study and a second quantitative RT-qPCR assay. The slope of the initial quantitative assay was - 3.321 with an efficiency of 100.04% and amplification factor equal to 2. Analysis of the repeatability data revealed a Limit of Quantification of 5 copies/reaction and Limit of Detection (95%) of 2.83 copies per reaction. In the diagnostic sensitivity tests, there was an accuracy of 97.37% when compared to the reference test. This assay proved to be highly efficient and reproducible, making it a valuable tool to monitor hepatitis Delta patients and assess the risk of disease progression, as well as the effectiveness of treatment.

Seroprevalence of antibodies against herpesvirus type 2 in a female prison population in Mato Grosso / Soroprevalência de anticorpos contra herpesvírus tipo 2 em população prisional feminina mato-grossense

Descrever a soroprevalência de anticorpos contra herpes vírus simples 2 em reeducandas de uma cadeia pública feminina de Mato Grosso no ano de 2016. Trata-se de um estudo transversal com abordagem quantitativa, realizado com 50 reeducandas reclusas de uma cadeia pública feminina de Mato Grosso. A coleta de dados foi realizada por meio de entrevista com 50 mulheres. Para determinar a soroprevalência da infecção por HSV-2, foram analisadas amostras de soro pelo método ELISA em busca de anticorpos do tipo IgG no Laboratório de Imunologia Viral do Instituto Oswaldo Cruz ­ RJ. A soroprevalência de HSV-2 encontrada na população avaliada foi de 80%, valor muito superior ao relatado na população geral brasileira e em outras estudos com populações prisionais em todo o mundo. O perfil das reeducandas predominou entre mulheres jovens, pardas, com baixa escolaridade, solteiras e com renda mensal baixa. O presente estudo encontrou alta soroprevalência de anticorpos contra HSV-2 nesta população. Esses dados fornecem importantes informações que podem auxiliar na implementação de ações efetivas que melhor previnam e controlem a herpes genital, bem como as demais ISTs em populações encarceradas.

Epidemiological Survey of Human Alphaherpesvirus 2 (HSV-2) Infection in Indigenous People of Dourados Municipality, Central Brazil.

Sexually transmitted Human alphaherpesvirus 2 (HSV-2) causes genital ulcers, especially among sexually active adolescents and adults. We estimated the exact prevalence of anti-HSV-2 antibodies and correlated it with the demographic and behavioral aspects of the Indigenous population of the Jaguapirú and Bororó villages (Dourados, Mato Grosso do Sul (MS), Brazil). In total, 1360 individuals (>18 years old) were administered serologic tests. The prevalence of anti-HSV-2 IgM was 12.9%, that of anti-HSV-2 IgG was 57.2%, and 8.5% cases tested positive for both HSV-2 IgM and IgG. The prevalence of anti-HSV-2 antibodies was higher in females (59.5%) compared to males (49%), with an OR of 0.64 (0.49-0.83). Anti-HSV-2 antibodies were found in 14.2%, 12.3%, 15.4%, and 14.5% of participants with urinary problems, genital wounds, genital warts, and urethral discharge, respectively. In summary, the seroprevalence of HSV-2 in the Indigenous population was five times higher than that reported in the general adult Brazilian population. Educational level, income level, smoking, condom use, incarceration, illicit drug abuse, the sharing of used needles and syringes without adequate disinfection, homosexual relationships, prostitution, the sexual practices among drug users, and avoidance of contraceptive methods could contribute to the facilitation of HSV-2 transmission in the Indigenous population. Our results may help develop culturally appropriate intervention programs that eliminate health-access barriers and improve the implementation of public health policies aimed at promoting information regarding and preventing, treating, and controlling HSV-2 infection in Brazilian Indigenous populations.

RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples.

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid method that can replace RT-qPCR. A simple molecular assay for SARS-CoV-2 RNA detection in gold-standard diagnosis through swabs and alternative specimens such as saliva could be helpful in promoting genomic surveillance. A multicenter study was conducted to evaluate the RT-LAMP assay method as an alternative for the molecular detection of SARS-CoV-2 lineages in swab and saliva samples. A total of 350 swabs from individuals with (n = 276) or without (n = 74) COVID-19 tested by RT-qPCR were collected. Paired saliva was also collected from 90 individuals who had SARS-CoV-2 RNA that was detectable (n = 30) or undetectable (n = 60) via RT-qPCR. For the RT-LAMP methodology, six primers were used for ORF1 gene amplification. As for SARS-CoV-2 genotyping, 39 swabs had the whole genome sequenced by MinION. The sensitivity of RT-LAMP to the swab was 90.2%. For the swab samples with Ct ≤ 30, the sensitivity improved by 96%. Considering saliva with Ct ≤ 30 in RT-qPCR testing, the RT-LAMP sensitivity was 100%. The RT-LAMP specificity was 100% for both the swab and saliva samples. This RT-LAMP assay was capable of detecting all the SARS-CoV-2 lineages circulating in the Brazilian swab samples. The RT-LAMP method has significant potential for use in clinical routines since it was capable of detecting SARS-CoV-2 RNA in swab and saliva samples.

High prevalence of hepatitis A and E viruses in environmental and clinical samples from West Argentina.

Environmental surveillance of water sources is important to monitoring viral hepatitis transmission in clinical settings. This study investigated the circulation of hepatitis A (HAV) and E (HEV) viruses in sewage and clinical samples from Argentina. Between 2016 and 2017, 80 raw sewage samples and 86 clinical samples (stool and serum) from suspected cases of hepatitis A and hepatitis E were obtained. HAV and HEV were tested by both real-time and nested PCR. Positive samples were sequenced for genotype determination and phylogenetic analysis. Overall, HAV was recovered in 39% of sewage samples and 61.1% of clinical samples. HEV was detected in 22.5% of sewage samples and 15.9% of clinical samples. HAV was found more frequently in sewage during the winter and in clinical samples in spring; HEV was more prevalent in sewage during summer and in clinical samples in autumn. All HAV isolates belonged to genotype IA and HEV isolates belonged to genotype 3, the most prevalent genotypes in South America. High prevalence of HAV and HEV in environmental and clinical samples in Mendoza, Argentina was observed. These findings reinforce the importance of environmental surveillance and implementation of health strategies to control the spread of HAV and HEV in developing countries.

High prevalence of hepatitis A and E viruses in environmental and clinical samples from West Argentina

ABSTRACT Environmental surveillance of water sources is important to monitoring viral hepatitis transmission in clinical settings. This study investigated the circulation of hepatitis A (HAV) and E (HEV) viruses in sewage and clinical samples from Argentina. Between 2016 and 2017, 80 raw sewage samples and 86 clinical samples (stool and serum) from suspected cases of hepatitis A and hepatitis E were obtained. HAV and HEV were tested by both real-time and nested PCR. Positive samples were sequenced for genotype determination and phylogenetic analysis. Overall, HAV was recovered in 39% of sewage samples and 61.1% of clinical samples. HEV was detected in 22.5% of sewage samples and 15.9% of clinical samples. HAV was found more frequently in sewage during the winter and in clinical samples in spring; HEV was more prevalent in sewage during summer and in clinical samples in autumn. All HAV isolates belonged to genotype IA and HEV isolates belonged to genotype 3, the most prevalent genotypes in South America. High prevalence of HAV and HEV in environmental and clinical samples in Mendoza, Argentina was observed. These findings reinforce the importance of environmental surveillance and implementation of health strategies to control the spread of HAV and HEV in developing countries.