Rotaviruses (RVs) have been identified as one of the main infectious causes of diarrhea in young pigs. We determined the prevalence of rotavirus A (RVA), C (RVC), and H (RVH) in pigs on a Brazilian farm. Samples were screened by reverse-transcription (RT)-PCR, and samples positive for RVA were genotyped by PCR amplification and sequencing analysis. Of the 329 fecal samples analyzed, 102 (30.9%) were positive for RV, 25 (7.6%) contained RVA only, 32 (9.7%) contained RVC only, and 31 (9.4%) contained RVH only. Co-circulation, the presence of ≥ 2 RVs in a sample, was detected in 14 (4.2%) samples. Of the 15 animals with diarrhea, 6 (40%) were positive for RV, and of the 314 asymptomatic animals, 96 (30.6%) were positive for RV; there was no statistically significant difference between the 2 groups ( p = 0.441). Genotyping of RVA strains showed co-circulation of genotypes G1, G3, G9-P[8]-I1, and I2-E1. Phylogenetic analysis showed that some of the RVA genotypes found in pigs had high percentages of identity when compared with reference strains from humans, which suggests interspecies transmission. Because RVs may be zoonotic, excretion of RVs into the environment can result in transmission to agricultural workers causing interspecies infections and allowing the emergence of new reassorted viruses.

The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike gene. Monitoring the S gene mutations is crucial for successful controlling measures and detecting variants that can evade vaccine immunity. Even after the costs reduction resulting from the pandemic, the new generation sequencing methodologies remain unavailable to a large number of scientific groups. Therefore, to support the urgent surveillance of SARS-CoV-2 S gene, this work describes a new feasible protocol for complete nucleotide sequencing of the S gene using the Sanger technique. Such a methodology could be easily adopted by any laboratory with experience in sequencing, adding to effective surveillance of SARS-CoV-2 spreading and evolution.

Background Rotavirus C (RVC) is an enteric pathogen that affects humans and animals around the world. Methods In this study, we characterized the genetic diversity of RVC strains detected in asymptomatic Brazilian pigs by sequencing the NSP4, NSP5 and VP6 genes. Results The results of reverse transcription polymerase chain reaction showed that 53 of 579 samples (9.2%) contained RVC. Positive samples were genotyped by sequencing gene segments NSP4, and NSP5. Most of the RCV strains encountered were classified into typically porcine genotypes: E1‐H1. In two strains, BP182 and BP208, the NSP4 gene grouped with E2‐RVC human strains with 94.2%–96.5% nucleotide identity, although the NSP5 gene was porcine‐like (H1). In strain SD67, the NSP5 gene grouped with human H2‐RVC with 92.5%–98.7% nucleotide identity and the NSP4 gene grouped with porcine strains (E1). Two strains (BP208 and SD67) were also genotyped by sequencing gene segment VP6. The VP6 gene grouped with porcine strains, I6 (89.3%–90.2% nucleotide identity) and I5 (88.7%–90.5% nucleotide identity), for strains BP208 and SD67, respectively. Conclusions These results are indicative of genomic reassortment between RVC strains of human and porcine origin. In recent years, the incidence of RVC infection among humans has increased significantly. It is important to measure the frequency of interspecies transmission in order to monitor the evolution of these viruses and to identify rearranged strains that may lead to an epidemic.

The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike protein. Monitoring the S protein mutations is crucial for successful controlling measures and detect variants that can evade vaccine immunity. Even after the costs reduction imposed by the pandemic, the new generation sequencing methodologies remain unavailable to many scientific groups. Therefore, to support the urgent surveillance of SARS-CoV-2 S protein, this work describes a protocol for complete nucleotide sequencing of the S protein using the Sanger technique. Thus, any laboratory with experience in sequencing can adopt this protocol.