Lack of molecular evidence of fecal-borne viruses in capybaras from São Paulo state, Brazil, 2018-2020: a minor public health issue.

Capybara (Hydrochoerus hydrochaeris) is the world's largest rodent species distributed throughout South America. These animals are incredibly tolerant to anthropogenic environments and are occupying large urban centers. Capybaras are known to carry potentially zoonotic agents, including R. rickettsia, Leishmania spp., Leptospira spp., Trypanosoma spp., Salmonella spp., Toxoplasma gondii, and rabies virus. Focusing on the importance of monitoring potential sources of emerging zoonotic viruses and new viral reservoirs, the aim of the present study was to assess the presence of fecal-borne viruses in the feces of capybaras living in urban parks in São Paulo state, Brazil. A total of 337 fecal samples were collected between 2018 and 2020 and screened for the following: (i) Rotavirus group A (RVA) by ELISA; (ii) non-RVA species and Picobirnavirus (PBV) using PAGE; (iii) Human Bocaparvovirus (HBoV), Bufavirus (BuV), Tusavirus (TuV), and Cutavirus (CuV) qPCR; (iv) Human Enterovirus (EV), Norovirus GII (NoV), and Hantavirus by in houses RT-qPCR; (v) SARS-CoV-2 via commercial RT-qPCR kit assay; and (vi) Astrovirus (AstV) and Adenovirus (AdV) using conventional nested (RT)-PCRs. All fecal samples tested were negative for fecal-borne viruses. This study adds further evidence that the fecal-borne viruses is a minor public health issue in Brazilian capybaras, at least during the surveillance period and surveyed areas. Continuous monitoring of sylvatic animals is essential to prevent and control the emergence or re-emergence of newly discovered virus as well as viruses with known zoonotic potential.

Norovirus GII.Pe Genotype: Tracking a Foodborne Outbreak on a Cruise Ship Through Molecular Epidemiology, Brazil, 2014.

Norovirus (NoV) is recognized as the most common cause of foodborne outbreaks. In 2014, an outbreak of acute gastroenteritis occurred on a cruise ship in Brazil, and NoV became the suspected etiology. Here we present the molecular identification of the NoV strains and the use of sequence analysis to determine modes of virus transmission. Food (cream cheese, tuna salad, grilled fish, orange mousse, and vegetables soup) and clinical samples were analyzed by ELISA, conventional RT-PCR, qRT-PCR, and sequencing. Genogroup GII NoV was identified by ELISA and conventional RT-PCR in fecal samples from 5 of 12 patients tested (41.7%), and in the orange mousse food sample by conventional RT-PCR and qRT-PCR. Two fecal GII NoV samples and the orange mousse GII NoV sample were successfully genotyped as GII.Pe (ORF 1), revealed 98.0-98.8% identities among them, and shared phylogenetically distinct cluster. Establishing the source of a NoV outbreak can be a challenging task. In this report, the molecular analysis of the partial RdRp NoV gene provided a powerful tool for genotyping (GII.Pe) and tracking of outbreak-related samples. In addition, the same fast and simple extraction methods applied to clinical samples could be successfully used for complex food matrices, and have the potential to be introduced in routine laboratories for screening foods for presence of NoV.

Rotavirus genotypes and the indigenous children of Brazilian midwest in the vaccine era, 2008-2012: Footprints of animal genome.

World group A rotavirus (RVA) surveillance data provides useful estimates of the disease burden, however, indigenous population might require special consideration. The aim of this study was to describe the results of G- and P-types from Brazilian native children ≤ 3 years. Furthermore, selected strains have been analyzed for the VP7, VP6, VP4, and NSP4 encoding genes in order to gain insight into genetic variability of Brazilian strains. A total of 149 samples, collected during 2008-2012, were tested for RVA using ELISA and PAGE, following by RT-PCR and sequencing. RVA infection was detected in 8.7% of samples (13/149). Genotype G2P[4] was detected in 2008 and 2010, G8P[6] in 2009, and G3P[8] in 2011. The phylogenetic analysis of the VP7 and VP4 genes grouped the Brazilian G2P[4] and G3P[8] strains within the lineages currently circulating in humans worldwide. However, the phylogenetic analysis of the VP6 and NSP4 from the Brazilian G2P[4] strains, and the VP7 and NSP4 from the Brazilian G3P[8] strains suggest a distant common ancestor with different animal strains (bovine, caprine, and porcine). The epidemiological and genetic information obtained in the present study is expected to provide an updated understanding of RVA genotypes circulating in the native infant population, and to formulate policies for the use of RVA vaccines in indigenous Brazilian people. Moreover, these results highlight the great diversity of human RVA strains circulating in Brazil, and an in-depth surveillance of human and animal RVA will lead to a better understanding of the complex dynamics of RVA evolution.

Rotavirus genotypes and the indigenous children of Brazilian midwest in the vaccine era, 2008-2012: footprints of animal genome

World group A rotavirus (RVA) surveillance data provides useful estimates of the disease burden, however, indigenous population might require special consideration. The aim of this study was to describe the results of G­ and P­types from Brazilian native children ≤3 years. Furthermore, selected strains have been analyzed for the VP7, VP6, VP4, and NSP4 encoding genes in order to gain insight into genetic variability of Brazilian strains. A total of 149 samples, collected during 2008­2012, were tested for RVA using ELISA and PAGE, following by RT­PCR and sequencing. RVA infection was detected in 8.7% of samples (13/149). Genotype G2P[4] was detected in 2008 and 2010, G8P[6] in 2009, and G3P[8] in 2011. The phylogenetic analysis of the VP7 and VP4 genes grouped the Brazilian G2P[4] and G3P[8] strains within the lineages currently circulating in humans worldwide. However, the phylogenetic analysis of the VP6 and NSP4 from the Brazilian G2P[4] strains, and the VP7 and NSP4 from the Brazilian G3P[8] strains suggest a distant common ancestor with different animal strains (bovine, caprine, and porcine). The epidemiological and genetic information obtained in the present study is expected to provide an updated understanding of RVA genotypes circulating in the native infant population, and to formulate policies for the use of RVA vaccines in indigenous Brazilian people. Moreover, these results highlight the great diversity of human RVA strains circulating in Brazil, and an in­depth surveillance of human and animal RVA will lead to a better understanding of the complex dynamics of RVA evolution

Rotavirus G2P[4] and G2P[4]+[6] infections during norovirus gastroenteritis outbreak: summer season 2010, Brazil.

INTRODUCTION: This study aimed to monitor the seasonality of rotavirus infection, and gain insight into the variability of Brazilian strains. METHODS: A total of 28 stool samples were analyzed from 698 revised cases of gastroenteritis during a norovirus outbreak in the summer of 2010 in Guarujá, Brazil. Diagnosis was performed using enzyme-linked immunosorbent assay (ELISA), reverse transcription polymerase chain reaction (RT-PCR), and sequencing. RESULTS: Rotavirus infection was detected in 17.9% (5/28) of samples; 4 samples were G2P[4] genotype, and one G2P[4]+P[6] genotype. G2 and P[4] sequences showed a genetic relationship to strains from India and Russia, respectively. CONCLUSIONS: The seasonal pattern of rotavirus may be a consequence of human activity apart from climate factors.

Rotavirus G2P[4] and G2P[4]+[6] infections during norovirus gastroenteritis outbreak: summer season 2010, Brazil

Introduction This study aimed to monitor the seasonality of rotavirus infection, and gain insight into the variability of Brazilian strains. Methods A total of 28 stool samples were analyzed from 698 revised cases of gastroenteritis during a norovirus outbreak in the summer of 2010 in Guarujá, Brazil. Diagnosis was performed using enzyme-linked immunosorbent assay (ELISA), reverse transcription polymerase chain reaction (RT-PCR), and sequencing. Results Rotavirus infection was detected in 17.9% (5/28) of samples; 4 samples were G2P[4] genotype, and one G2P[4]+P[6] genotype. G2 and P[4] sequences showed a genetic relationship to strains from India and Russia, respectively. Conclusions The seasonal pattern of rotavirus may be a consequence of human activity apart from climate factors. .

Norovirus 3rd Generation kit: an improvement for rapid diagnosis of sporadic gastroenteritis cases and valuable for outbreak detection.

The aim of this study was to evaluate the sensitivity and specificity of the Ridascreen(®) Norovirus 3rd Generation kit compared to the RT-PCR. A retrospective, descriptive study was conducted with 245 specimens from sporadic cases and outbreak surveillance samples of gastroenteritis in Brazil from 2006 to 2009. Overall, the kit showed a sensitivity of 61.8% and a specificity of 92.5%. The sensitivity for outbreaks diagnosis was 87.9% and specificity 83.8%. The Ridascreen(®) 3rd Generation could detect specimen containing genogroup (G) II with high sensitivity. However, GI and mixed infections (GI/GII) were unlikely to be detected by the kit. ELISA for Norovirus (NoV) detection provides a rapid, technically simple assay system that can be used to increase the surveillance of gastroenteritis outbreaks, especially in Public Health Laboratories with high sample throughput. This assay is useful for the detection of NoV outbreaks and is an improvement as compared to previous ELISAs; however, due to its sensitivity, RT-PCR in still required for routine NoV detection in sporadic cases investigation.