The emergence of SARS-CoV-2 P.1 lineage coincided with a surge in hospitalisations in the North region of Brazil. In the South region’s Rio Grande do Sul state, severe COVID-19 case numbers rose 3.8 fold in February 2021. During that month, at a COVID-19 referral hospital in this state, whole-genome sequencing of a subset of cases’ specimens (n = 27) revealed P.1 lineage SARS-CoV-2 in most (n = 24). Findings raise concerns regarding a possible association between lineage P.1 and rapid case and hospitalisation increases.

The present study performed a genetic identification of pestiviruses contaminating batches of fetal bovine serum (FBS) produced in Brazil from 2006 to 2014. Seventy-three FBS lots were screened by a RT-PCR targeting the 5’untranslated region (UTR) of the pestivirus genome. Thirty-nine lots (53.4%) were positive for pestivirus RNA and one contained infectious virus. Nucleotide sequencing and phylogenetic analysis of the 5’UTR revealed 34 lots (46.6%) containing RNA of bovine viral diarrhea virus type 1 (BVDV-1), being 23 BVDV-1a (5’ UTR identity 90.8-98.7%), eight BVDV-1b (93.9-96.7%) and three BVDV-1d (96.2- 97.6%). Six lots (8.2%) contained BVDV-2 (90.3-100% UTR identity) being two BVDV-2a; three BVDV-2b and one undetermined. Four FBS batches (5.5%) were found contaminated with HoBi-like virus (98.3 to 100%). Five batches (6.8%) contained more than one pestivirus. The high frequency of contamination of FBS with pestivirus RNA reinforce the need for systematic and updated guidelines for monitoring this product to reduce the risk of contamination of biologicals and introduction of contaminating agents into free areas.

RESUMO Este trabalho avaliou a imunogenicidade de vacinas para os herpesvírus bovino 1 e 5 (BoHV-1, BoHV-5) e vírus da diarreia viral bovina 1 e 2 (BVDV-1, BVDV-2), disponíveis no mercado brasileiro. Para isso, novilhos de raças de corte foram alocados em grupos de 10-12 animais e vacinados duas vezes (6/10, GMT 4,0 6/10, GMT 5,6 e 4/10, GMT 1,8 ABSTRACT This study evaluated the immunogenicity of vaccines for bovine herpesvirus 1 and 5 (BoHV-1/5) and viral diarrhea virus 1 and 2 (BVDV-1/2) available in the Brazilian market. Calves were divided into groups (10-12), vaccinated twice with a 30 days interval. Samples collected 30 days after the second dose were submitted to virus neutralization test against . Partial seroconversion to BVDV-1 was detected in four vaccine (6/10, GMT 4.0; 6/10, GMT 5.6 and 4/10, GMT 1.8). A vaccine induced response in only one animal and three vaccines did not induce antibodies against BVDV-1 in any animal. Antibodies to BVDV-2 were detected only in three vaccine groups, and partly (10/10, GMT 6.5; 5/10, GMT 1.6 and 2/10, GMT 1.0

Three dog shelters in Rio Grande do Sul were investigated for associations between the occurrence of respiratory viruses and shelter environmental conditions. Nasal secretions randomly collected during the cold season were tested via PCR, and this data collection was followed by nucleotide sequencing of the amplicons. In shelter #1 (poor sanitary and nutritional conditions, high animal density and constant contact between dogs), 78% (58/74) of the nasal samples were positive, 35% (26/74) of which were in single infections and 44% (32/74) of which were in coinfections. Shelters #2 and #3 had satisfactory sanitary and nutritional conditions, outdoors exercise areas (#2) and animal clustering by groups (#3). In shelter #2, 9% (3/35) of the samples were positive for Canine parainfluenza virus (CPIV), and 6% (2/35) were positive for Canid herpesvirus 1 (CaHV-1). In shelter #3, 9% (7/77) of the samples were positive for Canine adenovirus type 2 (CAdV-2), and 1% (1/77) were positive for Canine distemper virus (CDV). The amplicon sequences (CPIV and CDV nucleoprotein gene; CAdV-2 E3 gene; CaHV-1 glycoprotein B gene) showed 94–100% nucleotide identity with GenBank sequences. Our results demonstrate that CPIV, CAdV-2 and CDV are common in dog shelters and that their frequencies appear to be related with environmental and nutritional conditions. These results indicate the need for control/prevention measures, including vaccination and environmental management, to minimize these infections and improve dog health.

Bovine pestiviruses, e.g., bovine viral diarrhea virus types 1 (BVDV-1 or Pestivirus A), BVDV-2 (Pestivirus B), and HoBi-like pestiviruses (HoBiPeV or Pestivirus H), have been shown to circulate in Brazilian cattle in varied proportions. In this study, we identified genetically pestiviruses circulating in beef cattle in Rio Grande do Sul, the southern most Brazilian state. Screening of serum of 15.584 beef calves destined to be export by an antigen capture ELISA and, subsequently, by reverse-transcription polymerase chain reaction (RT-PCR), revealed 135 containing pestivirus RNA. Genetic typing of these viruses based on nucleotide sequencing and phylogenetic analysis of the 5′ untranslated region (5′ UTR) of the viral genome allowed for the identification of 90 different viruses, being 38 BVDV-1 (42.2%), 31 BVDV-2 (34.4%), and 21 HoBiPeV (23.4%). Among BVDV-1, only subtypes BVDV-1a (n = 28, 31.1%) and BVDV-1b (n = 10, 11.1%) were identified. All 31 BVDV-2 isolates belonged to BVDV-2b subtype and the 21 HoBiPeV viruses clustered to subgroup 3a. Thus, this study provides an approximate genetic profile of pestiviruses circulating in beef cattle in a traditional Brazilian beef cattle-raising state.

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The pestiviruses bovine viral diarrhea virus 1 (BVDV-1), 2 (BVDV-2), and HoBi-like (HoBiPeV) are endemic among Brazilian cattle, the world's largest commercial bovine herd. In the last two decades (1998–2018) over 300 bovine pestiviruses have been partially or fully sequenced in Brazil, including viruses from different regions, different epidemiological backgrounds, and associated with diverse clinical presentations. Phylogenetic analysis of these viruses demonstrated a predominance of BVDV-1 (54.4%), with subgenotypes −1a (33.9% of total) and −1b (16.3%) being more frequent and subgenotypes −1d, −1e, and −1i at very low frequencies. The overall BVDV-2 frequency was 25.7% but it varied largely by region, reaching up to 48% in Southern states. BVDV-2b was the predominant subgenotype (84.8% of BVDV-2), followed by BVDV-2a (8.86%). HoBiPeV accounted for 19.9% (61/307) of the genotyped viruses and were detected at high frequency in cattle from Northeastern states. These findings demonstrate a unique mix of pestivirus species and subgenotypes, unlike that seen in Europe or North America. The design of effective diagnostic tools, vaccines, and control programs for limiting bovine pestivirus infections in Brazil must take into consideration this unique mix of viruses. This article provides a critical review of two decades of genetic identification of pestiviruses in Brazil.

The pestiviruses bovine viral diarrhea virus 1 and 2 (BVDV-1 and -2, respectively) and HoBi-like pestivirus (HoBiPeV) are important pathogens of cattle, and a number of reverse-transcription PCR (RT-PCR)-based assays have been developed for their detection in clinical specimens. We evaluated a newly designed set of pan-bovine pestivirus primers (BP189-389) in a gel-based RT-PCR screening test for pestiviruses in the sera of beef calves destined for export from southern Brazil. Serum samples positive for BVDV antigens by an antigen ELISA (n = 135) were submitted to RT-PCR assays using different sets of primers, followed by nucleotide sequencing of the amplicons. RT-PCR with pestivirus primers 324-326 detected 110 positive samples: BVDV-1 (n = 62), BVDV-2 (n = 38), and HoBiPeV (n = 10). A PCR using primers HCV90-368 detected 97 positive samples (64 BVDV-1; 33 BVDV-2). An additional RT-PCR round using BVDV-2-specific primers (2F-2R) detected 45 positive samples (including 38 detected by primers 324-326 and 33 by HCV90-368); whereas a RT-PCR using HoBiPeV-specific primers (N2-R5) detected 26 positive samples (including 10 detected by primers 324-326).The assay using the primers BP189-389 detected all 135 ELISA-positive samples, including the 26 HoBiPeV detected by primers N2-R5. Our results demonstrated that primers BP189-389 compare favorably against other primer sets in the detection of bovine pestiviruses, especially HoBiPeV. This conventional PCR may be useful for efficient detection of pestiviruses in bovine sera and other specimens as well, especially in laboratories without real-time PCR equipment.