Characterization of Bovine Papillomavirus Types Detected in Cattle Rumen Tissues from Amazon Region, Brazil.

The Bos Taurus Papillomavirus, commonly known as bovine papillomavirus (BPV), can cause lesions in the mucosa of the gastrointestinal tract (GIT) in cattle and induce the formation of papillomas in organs such as the pharynx, esophagus, rumen and reticulum. GIT papillomas can lead to feeding and breathing distress. Moreover, the sample collection is challenging, which reduces the BPV diagnosis in these organs. BPV can cause exophytic nodular, cauliflower-like, flat, filiform or atypical-shape papillomas at the epidermis. Histologically, the papillomas demonstrate orthokeratotic/parakeratotic hyperkeratosis and koilocytosis and, currently, BPV comprises 45 described types. The aim of this study was to carry out the genetic characterization of BPV present in rumen neoplastic lesions of cattle raised extensively in the Western Amazon region, Brazil. A total of 100 papillomatous ruminal samples were collected from animals slaughtered in Ji-Paraná and Urupá municipalities from the Rondônia state, Brazil. The samples were submitted to PCR using the primer pair FAP59/FAP64 and sequenced by the Sanger method. Histopathological analysis was performed on 24 samples, which had enough material for this purpose. As a result, samples were histologically classified as fibropapilloma and squamous papilloma. Among the samples analyzed, it was possible to identify the BPVs 2, 13 (Delta PVs) and 44, with one sample classified as a putative new subtype of BPV44. The present study could identify BPV13 and 44 types in cattle rumen tissues from the Brazilian Amazon region for the first time.

Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolution in an Immunodeficient Child.

BACKGROUND: With the progression of the Coronavirus disease pandemic, the number of mutations in the viral genome has increased, showing the adaptive evolution of severe acute respiratory syndrome coronavirus 2 in humans and intensification in transmissibility. Long-term infections also allow the development of viral diversity. In this study, we report the case of a child with severe combined immu presenting a prolonged severe acute respiratory syndrome coronavirus 2 infection. We aimed to analyze 3 naso-oropharyngeal swab samples collected between August and December 2021 to describe the amino acid changes present in the sequence reads that may have a role in the emergence of new viral variants. METHODS: The whole genome from clinical samples was sequenced through high throughput sequencing and analyzed using a workflow to map reads and then find variations/single-nucleotide polymorphisms. In addition, the samples were isolated in cell culture, and a plaque forming units assay was performed, which indicates the presence of viable viral particles. RESULTS: The results obtained showed that the virus present in all samples is infectious. Also, there were 20 common mutations among the 3 sequence reads, found in the ORF1ab and ORF10 proteins. As well, a considerable number of uncommon mutations were found. CONCLUSIONS: In conclusion, we emphasize that genomic surveillance can be a useful tool to assess possible evolution signals in long-term patients.

Brief dispersion of a putative B.1.1.28-derived SARS-CoV-2 lineage harboring additional N234P and E471Q spike protein mutations in individuals crossing the Argentina-Brazil border.

BACKGROUND: SARS-CoV-2, the virus that causes COVID-19, is constantly mutating, leading to new variants that culminate in a temporal lineages fluctuation. B.1.1.28 lineage has been evolving in Brazil since February 2020 and originated P.1 (VOC), P.2 (VOI) and other P.Xs proposed as new variants. METHODS AND RESULTS: In this study, through the Illumina platform, we performed the whole-genome sequencing of 26 positive samples of SARS-CoV-2. Employing variant calling analysis on FASTQ reads and phylogenetic inference, we report a brief dispersion of a potentially new B.1.1.28-derived variant detected between 2021 May and June in individuals crossing the border between Brazil and Argentina, and local spread to inpatients from hospitals at the Rio Grande do Sul state capital (Porto Alegre). Besides, the Rio Grande do Sul State SARS-CoV-2 genomic epidemiological data was analyzed and showed an important B.1.1.28 peak in RS at the same period (May-June), even in the presence of a major Gamma wave. CONCLUSIONS: The emergence of a putative B.1.1.28-derived lineage was identified in travelers crossing Brazil-Argentina border representing an important peak of B.1.1.28 in RS State with a decreased in Gamma variant frequency in the same period of time.