Impact of rotavirus vaccine on rotavirus genotypes and caliciviruses circulating in French cattle

Molecular Epidemiology of Rotavirus A in Calves: Evolutionary Analysis of a Bovine G8P[11] Strain and Spatio-Temporal Dynamics of G6 Lineages in the Americas

Rotavirus A (RVA) causes diarrhea in calves and frequently possesses the G6 and P[5]/P[11] genotypes, whereas G8 is less common. We aimed to compare RVA infections and G/P genotypes in beef and dairy calves from major livestock regions of Argentina, elucidate the evolutionary origin of a G8 strain and analyze the G8 lineages, infer the phylogenetic relationship of RVA field strains, and investigate the evolution and spatio-temporal dynamics of the main G6 lineages in American countries. Fecal samples (n = 422) from diarrheic (beef, 104; dairy, 137) and non-diarrheic (beef, 78; dairy, 103) calves were analyzed by ELISA and semi-nested multiplex RT-PCR. Sequencing, phylogenetic, phylodynamic, and phylogeographic analyses were performed. RVA infections were more frequent in beef (22.0%) than in dairy (14.2%) calves. Prevalent genotypes and G6 lineages were G6(IV)P[5] in beef (90.9%) and G6(III)P[11] (41.2%) or mixed genotypes (23.5%) in dairy calves. The only G8 strain was phylogenetically related to bovine and artiodactyl bovine-like strains. Re-analyses inside the G8 genotype identified G8(I) to G8(VIII) lineages. Of all G6 strains characterized, the G6(IV)P[5](I) strains from "Cuenca del Salado" (Argentina) and Uruguay clustered together. According to farm location, a clustering pattern for G6(IV)P[5] strains of beef farms was observed. Both G6 lineage strains together revealed an evolutionary rate of 1.24 × 10-3 substitutions/site/year, and the time to the most recent common ancestor was dated in 1853. The most probable ancestral locations were Argentina in 1981 for G6(III) strains and the USA in 1940 for G6(IV) strains. The highest migration rates for both G6 lineages together were from Argentina to Brazil and Uruguay. Altogether, the epidemiology, genetic diversity, and phylogeny of RVA in calves can differ according to the production system and farm location. We provide novel knowledge about the evolutionary origin of a bovine G8P[11] strain. Finally, bovine G6 strains from American countries would have originated in the USA nearly a century before its first description.

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.

G and P genotype profiles of rotavirus A field strains circulating in a vaccinated bovine farm as parameters for assessing biosecurity level

After improvement of hygiene protocols on boots in a bovine operation (farm A) in Ibaraki, Japan in September 2017, mortality of calves and the detection of 4 viral pathogen indicators, including bovine rotavirus A (RVA), became significantly low for one year. Subsequently, in the present study, these indicators and mortality were monitored and confirmed all were still low, except for the detection rate of bovine RVA in calves less than 3 weeks old. The present study aimed to investigate G and P genotypic profiles of RVAs in farm A from 2018 to 2020. Molecular analysis using semi-nested multiplex RT-PCR of positive RVAs (n=122) and sequencing of selected samples revealed the presence of G6, G8, G10, P[1], P[5] and P[11] genotypes and the prevalence of G and/or P combination and mixed infections. The most common combination of G and P types was G10P[11] (41.8%), followed by mixed infection with G6+G10P[5] (11.5%). Phylogenetic analysis of RVAs showed clustering with bovine and other animal-derived RVA strains, suggesting the possibility of multiple reassortant events with strains of bovine and others animal origins. Noteworthy as well is that vaccinated cattle might fail to provide their offspring with maternal immunity against RVA infections, due to insufficient colostrum feeding. Our findings further highlight the importance of RVA surveillance in bovine populations, which may be useful to improving effective routine vaccination and hygiene practices on bovine farms.

Occurrence and genetic diversity of rotavirus A in faeces of diarrheic calves submitted to a veterinary laboratory in Spain

A total of 237 faecal specimens from diarrheic calves younger than two months were collected and submitted for diagnosis of enteropathogens over a two-year period (2017-2018) to a veterinary laboratory. Samples originated from 193 dairy and beef farms in 29 provinces distributed throughout Spain, and were tested for the occurrence of three target enteric pathogens by reverse transcription real-time PCR (RT-qPCR): bovine rotavirus A (RVA), Cryptosporidium parvum and bovine coronavirus (BCoV). RT-PCR and nucleotide sequencing analysis were used to determine the G (VP7 gene) and P (VP4 gene) genotypes of 26 specimens positive for RVA. A total of 188 specimens (79.3 %) were positive for at least one of the three target enteric pathogens, and 101 samples (42.6 %) harbored mixed infections. The individual prevalence was 57.8 %, 50.6 % and 23.6 % for C. parvum, RVA and BCoV, respectively. Molecular analysis of selected RVA strains revealed the presence of the G6, G10, G3, P[5] and P[11] genotypes, with the combinations G6P[5] and G6P[11] being the most prevalent. Alignments of nucleotide sequences of the VP7 and VP4 markers showed a high frequency of single nucleotide polymorphisms (SNPs), with up to 294 SNPs found in 869bp of sequence at the G6 genotype (0.338 SNPs/nt), which reveals the extensive genetic diversity of RVA strains. Phylogenetic analysis of the VP7 gene of the G6 strains revealed four distinct lineages, with most strains clustering in the G6-IV lineage. The discrepancies between the RVA genotypes circulating in the sampled cattle farms and the genotypes contained in commercial vaccines currently available in Spain are discussed. We believe that this is the first study on the molecular characterization of rotavirus infecting cattle in Spain.

Animals as Reservoir for Human Norovirus

Norovirus is the most common cause of non-bacterial gastroenteritis and is a burden worldwide. The increasing norovirus diversity is currently categorized into at least 10 genogroups which are further classified into more than 40 genotypes. In addition to humans, norovirus can infect a broad range of hosts including livestock, pets, and wild animals, e.g., marine mammals and bats. Little is known about norovirus infections in most non-human hosts, but the close genetic relatedness between some animal and human noroviruses coupled with lack of understanding where newly appearing human norovirus genotypes and variants are emerging from has led to the hypothesis that norovirus may not be host restricted and might be able to jump the species barrier. We have systematically reviewed the literature to describe the diversity, prevalence, and geographic distribution of noroviruses found in animals, and the pathology associated with infection. We further discuss the evidence that exists for or against interspecies transmission including surveillance data and data from in vitro and in vivo experiments.

Longitudinal surveillance of rotavirus A genotypes circulating in a high milk yield dairy cattle herd after the introduction of a rotavirus vaccine

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RVA vaccination program reduces the frequency and intensity of diarrhea in dairy calves.

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The vaccination immune pressure can select specific genotypes in RVA field strains.

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RVA genotype G10P[11] in fecal samples of calves from G6P[5] vaccinated dairy cattle herds.

Worldwide, neonatal diarrhea is one of the most important health issues affecting dairy calves, and rotavirus A (RVA) is one of its primary causes. Among the measures to mitigate the risk of diarrhea outbreaks, cow vaccination stands out as one of the most important. However, the immune pressure resulting from routine vaccination may be able to select specific G and P genotypes in RVA field strains. This study aimed to determine the frequency and intensity of neonatal diarrhea and the incidence of RVA and attempted to monitor the G and P genotypes present in the RVA strains circulating in a high milk yield cattle herd vaccinated with RVA G6P[5] strain. Fecal samples (n = 1220) from 122 Holstein heifer calves between 0–30 days old that were born from RVA-vaccinated cows were collected at 10 different time points, regardless of the presence or absence of diarrhea. The presence of RVA in fecal samples was determined by the polyacrylamide gel electrophoresis (PAGE) technique and confirmed by reverse transcription polymerase chain reaction (RT-PCR). G and P amplicons from 10 RVA-positive fecal samples from calves of different ages and collections were subjected to nucleotide sequencing. The proportion of the calves and fecal samples that were positive for RVA were 62.3% (76/122) and 8.1% (99/1220), respectively. Using sequence analysis, all 10 RVA field strains presented genotype G10P[11]. The protection of G6P[5] vaccination is clear, as this genotype was not detected in this study, and it is known that vaccination against RVA reduces the incidence of diarrhea independent of genotype involved. This result demonstrates the importance of epidemiological monitoring of RVA genotypes circulating in vaccinated dairy cattle herds to the early detection of new potential pathogenic RVA strains.

Molecular prevalence of bovine noroviruses and neboviruses in newborn calves in Iran

In this study, bovine enteric caliciviruses (BECs) were detected in 49.4% of a total of 253 stool specimens for diarrheic calves collected from 42 industrial dairy farms from March 2010 to February 2012. Genogroup III norovirus (NoVsGIII) were more prevalent (39.5%) than neboviruses (NBs) (15%), and coinfections were observed in 5.1% of the samples tested. Sequence analysis of the partial polymerase gene from 13 NoVsGIII samples indicated the circulation of both genotype 1 and genotype 2 strains. Among the six NB strains sequenced, five were related to the Bo/Nebraska/80/US strain, while one was related to the Bo/Newbury1/76/UK strain.

Farmed and companion animals as reservoirs of zoonotic rotavirus strains

Rotavirus (RV) infections are a major epidemiological problem in humans and farm animals. So far, a number of human and animal RV strains have been identified. Based on the antigenic properties of the VP6 capsid protein, they have been classified into eight serogroups (A-H). The most important of them are viruses from group A (RVA), which are responsible for more than 90% of cases of rotaviral diarrhoea. The segmented structure of the virus genome and the presence of animals in human neighbourhood favour genetic reassortment between RV strains originating from different hosts. This could result in an emergence of zoonotic virus strains. The increasing number of human infections caused by virus strains having genotypes which have only been identified in animals indicates the need for epidemiological surveillance of infections. Additionally, the identification of epidemic virus strains in the outbreaks of disease in humans should be conducted. The identification of RVA strains circulating in humans and animals will allow the assessment of the impact of vaccination on the selection and emergence of zoonotic RVA strains.

1. Introduction. 2. General characteristics and classification of rotaviruses. 3. Group A rotavirus infection in humans. 4. Group A rotavirus infection in animals. 5. Genetic changes and reassortment as factors leading to the formation of zoonotic rotavirus strains. 6. Impact of human immunization on changes in genotype profile of circulating rotavirus strains. 7. Conclusions

Longitudinal study of bovine rotavirus group A in newborn calves from vaccinated and unvaccinated dairy herds

Reports of rotavirus excretion in calves usually result from cross-sectional studies, and in face of the conflicting results regarding protection of calves born to vaccinated dams against diarrhea, the aim of the present study was to evaluate rotavirus excretion in dairy calves born to vaccinated or unvaccinated dams, to identify the genotypes of bovine rotavirus group A (RVA) strains isolated from these animals as well as to investigate characteristics of the disease in naturally occurring circumstances throughout the first month of life. Five hundred fifty-two fecal samples were taken from 56 calves, 28 from each farm and, in the vaccinated herd, 11/281 samples (3.91%) taken from six different calves tested positive for RVA while in the unvaccinated herd, 3/271 samples (1.11%) taken from 3 different calves tested positive. The genotyping of the VP7 genes showed 91.2% nucleotide sequence identity to G6 genotype (NCDV strain), and for the VP4 gene, strains from the vaccinated herd were 96.6% related to B223 strain, while strains from the unvaccinated herd were 88% related to P[5] genotype (UK strain). Genotypes found in this study were G6P[11] in the vaccinated herd and G6P[5] in the unvaccinated herd. All calves infected with rotavirus presented an episode of diarrhea in the first month of life, and the discrepancy between the genotypes found in the commercial vaccine (G6P[1] and G10P[11]) and the rotavirus strains circulating in both vaccinated and unvaccinated herds show the importance of keeping constant surveillance in order to avoid potential causes of vaccination failure.

Putative vaccine breakthrough event associated with heterotypic rotavirus infection in newborn calves, Turkey, 2015

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The circulation of G8 RVA strains in calves with diarrhea detected first time in Turkey.

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First report on whole genome of G8P[5] RVA strains from calves with diarrhea in Turkey.

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VP7 gene of the both Turkish bovine RVA strains showed the closest with human RVA strains detected in Europe and Africa.

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The genotype constellation of the strains is G8-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3.

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The findings raise provocative questions related to strain-specific vaccine effectiveness in herds where commercial RVA vaccines are routinely utilized.

Group A rotaviruses (RVA) are regarded as major enteric pathogens of large ruminants, including cattle. Rotavirus vaccines administered to pregnant cows are commonly used to provide passive immunity that protects newborn calves from the clinical disease. In this study we report the detection of RVA from calves with severe diarrhea in a herd regularly vaccinated to prevent enteric infections including RVA. Diarrheic disease was observed in newborn calves aged 4–15 days, with high morbidity and mortality rates, but no diarrhea was seen in adult animals. Rotavirus antigen was detected by enzyme-immunoassay in the intestinal content or the fecal samples of all examined animals. Besides RVA, bovine coronavirus and bovine enteric calicivirus were detected in some samples. Selected RVA strains were characterized by whole genome sequencing. Two strains, RVA/Cow-wt/TUR/Amasya-1/2015/G8P[5] and RVA/Cow-wt/TUR/Amasya-2/2015/G8P[5] were genotyped as G8-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3 and showed >99% nucleotide sequence identity among themselves. This genomic constellation is fairly common among bovine RVA strains; however, phylogenetic analysis of the G8 VP7 gene showed close genetic relationship to some European human RVA strains (up to 98.4% nt identity). Our findings is the first indication regarding the circulation of G8 RVA strains in Turkey. Given that the administered RVA vaccines contained type G6 and G10 VP7 antigens some concerns raised with regard to the level of heterotypic protection elicited by the vaccine strains against circulating bovine G8 RVA strains. Enhancement of surveillance of circulating RVA strains in calves across Turkey is needed to support ongoing vaccination programs.

The molecular epidemiology of bovine rotaviruses circulating in Iran: a two-year study

Bovine group A rotavirus (bovine RVA) is recognized as a major cause of severe gastroenteritis in newborn calves. The purpose of this study was to estimate the prevalence and identify the genotypes of circulating bovine RVA in newborn diarrheic calves. Two hundred fifty-three stool samples of diarrheic calves up to 1 month old were collected from 42 industrial dairy farms in two Iranian provinces during March 2010 to February 2012. All collected samples were screened for the presence of bovine RVA by RT-PCR, and the G and P genotypes were determined by semi-nested multiplex RT-PCR assay. The results of RT-PCR indicated that 49.4 % (125 out of 253) of the samples were positive for bovine RVA. The G and P genotyping of a subset of positive samples (n = 85) by semi-nested multiplex RT-PCR revealed that G6 (55.3 %) and G10 (43.5 %) and P[5] (51.8 %) and P[11] (27 %) were the most prevalent G and P genotypes, respectively. G6P[5] was the dominant genotype (35.3 %), followed by G10P[5], G10P[11] and G6P[11], with prevalence rates of 16.5 %, 15.3 % and 10.6 %, respectively. Sequence analysis of 20 VP7 and four VP4 genes showed highest nucleotide sequence identity with the corresponding genes of strains RVA/Cow-tc/GBR/UK/1973/G6P7[5] and RVA/Cow-tc/USA/B223/XXXX/G10P[11]. The results of this study reveal the diversity of G and P genotypes in bovine RVA samples from diarrheic Iranian calves and expands our knowledge of bovine RVA infections in the Middle East. These results also highlight the importance of producing of an effective rotavirus vaccine and its inclusion in the national cattle immunization program.

Detection and characterisation of bovine rotavirus in Ireland from 2006-2008

Background

Worldwide, Group A bovine rotavirus (RVA boRV) is one of the main causes of neonatal calf diarrhoea. Currently, limited epidemiological and sequence data exists on the RVA disease in bovines in Southern Ireland only. The aim of the study was to generate epidemiological and sequence data of RVA boRV distributed over a wide geographical area in Ireland.

Findings

272 stool samples were obtained from symptomatic calves and analysed to identify the prevalent G and P genotypes. Viral type combinations including G6P[5], G6P[11] and G10P[11] genotype were the most frequently identified. The G6P[5] combination was predominant throughtout the study, accounting for 70% (n = 191). Sequence analysis of the VP7 gene revealed that Irish G6 strains fell within Lineage IV, similiar to previous reports in Ireland.

Conclusion

The detection of unusual G and P combinations may have an impact on rotavirus control programmes and current vaccines may need to incorporate new strains, as the current vaccine available may not offer protection against all of these circulating types.