Cross-sectional study of the G and P genotypes of rotavirus A field strains circulating in regularly vaccinated dairy cattle herds

Genome analyses of species A rotavirus isolated from various mammalian hosts in Northern Ireland during 2013-2016

Rotavirus group A (RVA) is the most important cause of acute diarrhoea and severe dehydration in young mammals. Infection in livestock is associated with significant mortality and economic losses and, together with wildlife reservoirs, acts as a potential source of zoonotic transmission. Therefore, molecular surveillance of circulating RVA strains in animal species is necessary to assess the risks posed to humans and their livestock. An RVA molecular epidemiological surveillance study on clinically diseased livestock species revealed high prevalence in cattle and pigs (31 per cent and 18 per cent, respectively) with significant phylogenetic diversity including a novel and divergent ovine artiodactyl DS-1-like constellation G10-P[15]-I2-R2-C2-M2-A11-N2-T6-E2-H3. An RVA gene reassortment occurred in an RVA asymptomatic pig and identified as a G5-P[13] strain, and a non-structural protein (NSP)2 gene had intergenomically reassorted with a human RVA strain (reverse zoonosis) and possessed a novel NSP4 enterotoxin E9 which may relate to the asymptomatic RVA infection. Analysis of a novel sheep G10-P[15] strain viral protein 4 gene imparts a putative homologous intergenic and interspecies recombination event, subsequently creating the new P[15] divergent lineage. While surveillance across a wider range of wildlife and exotic species identified generally negative or low prevalence, a novel RVA interspecies transmission in a non-indigenous pudu deer (zoo origin) with the constellation of G6-P[11]12-R2-C2-M2-A3-N2-T6-E2-H3 was detected at a viral load of 11.1 log10 copies/gram. The detection of novel emerging strains, interspecies reassortment, interspecies infection, and recombination of RVA circulating in animal livestock and wildlife reservoirs is of paramount importance to the RVA epidemiology and evolution for the One Health approach and post-human vaccine introduction era where highly virulent animal RVA genotypes have the potential to be zoonotically transmitted.

Molecular surveillance of rotavirus A associated with diarrheic calves from the Republic of Korea and full genomic characterization of bovine-porcine reassortant G5P[7] strain

Group A rotavirus (RVA) is the most common diarrhea-causing pathogen among humans and animals worldwide. Rotavirus infection in neonatal calves causes major problems in the livestock industry. This study aimed to determine the prevalence and genetic diversity of bovine rotavirus (BoRVA) infections in calves with diarrhea and to perform whole genome analysis of an unusual strain, designated as RVA/Calf-wt/KOR/KNU-GJ2/2020/G5P[7], that was detected in a 2-day-old diarrheic calf. From 459 diarrheic calves aged 1-40 days, fecal samples were collected and BoRVA infections were screened using real-time RT-PCR targeting VP6 gene. BoRVA was detected in 195 (42.4%) samples and was most prevalent in calves aged 1-10 days (47.2%). No significant difference in the BoRVA infection rate was observed between calves born in herds that were (42.1%) and were not (42.6%) vaccinated against BoRVA. A binomial regression analysis revealed that calves aged 1-10 days (95% confidence intervals [CI]:1.18-24.34; P = 0.000) and 11-20 days (95% CI: 0.76-16.83, P = 0.000) had a 5.37- and 3.58-fold higher BoRVA prevalence in comparison to those aged 31-40 days, respectively. The RVA-positive samples were subsequently subjected to amplification of the VP7 and VP4 genes for determining G and P genotypes. Overall, 45 (23.1%, 45/195) and 63 (32.3, 63/195) sequences for VP7 and VP4 were obtained. In this study, four G and three P genotypes were identified. G6 (86.7%) was the most prevalent genotype, followed by G8 (8.9%), G10 (2.2%), and G5 (2.2%). P[5] (92.1%) was the most frequently detected, followed by P[11] (6.3%), and P[7] (1.6%). The G6P[5] (82.2%) is the most common combination found in Korean native calves with diarrhea, whereas G6P[11] (4.4%) and G10P[11] (2.2%) had relatively low prevalence. G8P[5] (8.9%) was identified for the first time in diarrheic calves in the KOR. The uncommon strain KNU-GJ2 exhibited a G5-P[7]-I5-R1-C1-M2-A1-N1-T1-E1-H1 genotype constellation possessing a typical porcine RVA backbone, with the exception of the VP3 gene, which is derived from bovine. Phylogenetically, except for VP3, ten gene segments of KNU-GJ2 were closely related to porcine, porcine-like, and reassortant bovine strains. Interestingly, the VP3-M2 gene of KNU-GJ2 clustered with bovine-like strains as well as reassortant porcine and bovine strains. Comparison of the NSP4s within a species-specific region of amino acids 131-141 demonstrated that KNU-GJ2 belonged to genotype B with porcine RVAs; however, it differed from porcine RVAs by one to three amino acids. The present study is fundamental to understanding the epidemiology and genotypes of circulating RVAs throughout the KOR and underscoring the importance of continuous monitoring and molecular characterization of RVAs circulating within animal populations for future vaccine development.

Rotaviruses A and C in dairy cattle in the state of Rio de Janeiro, Brazil

Stool samples were collected from calves from nine family-based small dairy farms in the state of Rio de Janeiro, for detection and characterization of rotavirus (RV) species A, B, and C (RVA, RVB, and RVC, respectively) by reverse transcription polymerase chain reaction. Twenty-six samples (27.7%) were positive for at least one of the species: 22 (23.4%) samples were positive only for RVA, 3 (3.2%) were positive for RVC, and one sample (1.1%) had co-infection of RVA and RVC. RVB was not detected. Seven (21.9%; n = 32) animals with diarrhea and 19 (30.1% n = 62) asymptomatic animals were positive, with no significant difference in positivity (p = 0.3677). RV was detected in all properties studied, at rates between 14.3 and 80%, demonstrating the widespread circulation of RV in four of the seven geographic regions of the state of Rio de Janeiro. Infection was more prevalent among animals ≤ 6 months of age. Sequence analysis of a portion of the RVA VP6-encoding gene identified the I2 genotype. RVC was also detected; to our knowledge, this is the first description of this agent in cattle in Brazil. The data presented here should add knowledge regarding the importance and prevalence of RV in our national territory, and may facilitate the planning and implementation of control and prevention measures for bovine rotavirus infections in Brazil.

Implementation of a pre-calving vaccination programme against rotavirus, coronavirus and enterotoxigenic Escherichia coli (F5) and association with dairy calf survival

Background

Diarrhea is one of the most common diseases and causes of death in calves during the first month of life. Pre-calving vaccination programme (PVP) against the most common diarrhea-causing pathogens could help to avoid this threat if hyperimmune transition milk (TM) is fed to calves throughout the whole susceptibility period. The aim of this retrospective cohort study was to reveal the implementation practices of PVPs in large commercial dairy farms and to compare calf-level mortality hazards during the first year of vaccination (V+ period) and a year before implementing the vaccination programme (V- period). A questionnaire was filled out in 15 large-scale dairy farms in Estonia that used PVP. The farms were assigned into three groups based on compliance with the vaccine directions for use and TM feeding practices. Calf-level time-to-event data was analyzed with an observation period of 21 days and on-farm mortality due to diarrhea being the event of interest.

Results

During the V+ period, a significant decline in diarrhea-induced calf mortality was identified in three out of six herds that followed vaccination instructions and fed TM for at least 14 days. On average, calf mortality hazard due to diarrhea decreased among these herds (hazard rate ratio (HR) = 0.72, 95% confidence interval (CI) 0.63; 0.81). In the group of correctly vaccinating herds where TM was fed for less than 14 days, diarrhea-induced calf mortality decreased in two herds and remained unchanged in two herds with average diarrhea-induced calf mortality hazard declining significantly during the vaccination period (HR = 0.24, 95% CI 0.14; 0.41). Among the three farms that deviated from the vaccination instructions, the average calf mortality hazard increased in the V+ period (HR = 1.61, 95% CI 1.21; 2.14).

Conclusions

This study revealed that implementing a PVP might aid to reduce diarrhea-induced calf mortality in large commercial dairy farms. There is a need to increase veterinarians´ and farmers´ awareness about the importance of including pregnant heifers into the vaccination programme and emphasize the importance of prolonged feeding of hyperimmune TM to calves.

Isolation and Characterization of Bovine RVA from Northeast China, 2017-2020

Group A rotaviruses (RVAs) are major enteric pathogens causing infections in calves. To investigate the epidemiological characteristics and genetic diversity of bovine rotavirus (BRV), 233 fecal samples were collected from calves with diarrhea in northeast China. The samples were analyzed for sequences encoding the inner capsid protein VP6 (subgroup) and the outer capsid proteins VP7 and VP4 (G and P type, respectively) using RT-PCR. Ten of the 233 samples (4.3%) were identified as BRV positive and were used for virus isolation and sequence analysis, revealing that all strains analyzed were of the G6P[1] genotype. The isolates exhibited high VP6 sequence identity to the USA cow RVA NCDV strain (>99% amino acid identity) and were further shown to be closely related to Japanese cow RVA BRV101 and Israelian human RVA G6P[1] strains, with >99% amino acid identity to VP7 and VP4 proteins, respectively. Comparative analyses of genome-predicted amino acid sequences between the isolates and the NCDV strains indicated that the antigenicity and infectivity of the strains isolated had changed. In this study, BRV genotypes and the genetic diversity among vaccinated cattle herds were monitored to provide epidemiological data and references for early diagnosis, allowing for early detection of new, potentially pathogenic RVA strains.

Genotype constellation of a rotavirus A field strain with an uncommon G8P[11] genotype combination in a rotavirus-vaccinated dairy cattle herd

In this report we describe the genotype constellation of a bovine rotavirus A (RVA) strain with an uncommon G8P[11] genotype combination. The RVA/Cow-wt/BRA/Y136/2017/G8P[11] strain was classified as G8-P[11]-I2-R5-C2-M2-A3-N2-T9-E2-H3. Phylogenetic analysis based on the VP7 gene showed that the Y136 strain and a human G8P[1] strain comprise a putative new (VII) lineage for the G8 genotype. In addition, two other genotypes, R5 (VP1) and T9 (NSP3), were identified in the constellation of Y136 that are rarely found in RVA strains of bovine origin. The immunological pressure caused by regular vaccination of cows might be responsible for the selection of heterologous RVA strains.

Identification of rotavirus A strains in small ruminants: first detection of G8P[1] genotypes in sheep in Turkey

Although members of rotavirus group A (RVA) are major enteric pathogens of humans and animals of many species, their impact on the health of small ruminants is not well documented. In this study, we conducted a molecular analysis of VP4, VP7, VP6 and NSP4 genes of RVAs detected using a commercial antigen ELISA in small ruminants with or without diarrhea in Turkey. Of the RVAs detected in sheep, one strain (Kutahya) was characterized as genotype G8P[1]-I2-E2. Two others (Ankara-1 and Ankara-2) were identified as NSP4 E2 and VP6 I2 genotypes, although they were untyped for the VP4 and VP7 genes. The RVAs from two goats were characterized as genotype G6P [1]-I2-E2. This is the first detection of in goats RVA genotypes G6P [1], which had previously only been found in cattle in Turkey, and of RVA in sheep. The study extends our current knowledge about the circulation of two RVA G genotypes, G6 and G8, in goat herds, and the detection of the G8 genotype in sheep in Turkey. This provides further information about the molecular epidemiology of RVAs in different animal species and indicates that additional surveillance programs are needed to determine the epidemiology of RVA in small ruminants and other species.