In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P [18] [12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to nonequine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines. INTRODUCTIONEquine group A rotavirus (RVA) strains were first detected in diarrhoeic foals in England in 1975(Flewett et al., 1975 and are a major cause of dehydrating diarrhoea in young 3Present address: Deltamune (Pty) Ltd, 248 Jean Avenue, Lyttelton, Centurion, 0140, South Africa.The GenBank/EMBL/DDBJ accession numbers for the equine rotavirus strains described in this study are JF712555-JF712565, JF712566-JF712576, JF712577-JF712587, JN872865-JN872875, JQ345489-JQ345499 and JN903507-JN903528. foals (Browning & Begg, 1996;Frederick et al., 2009; Imagawa et al., 1991;Saif et al., 1994). Serological data from Japan, the USA and France suggest that RVA is a ubiquitous pathogen in horse populations (Conner & Darlington, 1980;Imagawa et al., 1982;Pearson et al., 1982;Takahashi et al., 1979).RVA strains are icosahedral, non-enveloped viruses possessing a genome of 11 segments of dsRNA. The two outer capsid proteins, VP7 and VP4, elicit neutralizing antibodies independently and are used to differentiate RVA strains into G-types (glycoprotein) and P-types (proteasesensitive), respectively (Ciarlet & Estes, 2002 (Browning et al., 1991a). L338 was shown to possess the unique G13 and P[18] genotypes and a highly divergent NSP1 gene sequence, and to be distinct from other human and animal RVA strains by using RNA-RNA hybridization assays (Browning et al., 1991a; Iša & Snodgrass, 1994;Kojima et al., 1996;Taniguchi et al., 1994;Wu et al., 1993). In addition, a limited number of porcine-, bovineand feline-like RVA strains have been detected in horses. Examples include the G5P [7] RVA strain RVA/Horse-tc/ ...

Bovine coronavirus (BCoV) is an important viral pathogen associated with neonatal calf diarrhea. Our aim was to investigate the incidence of BCoV in diarrhea outbreaks in beef and dairy herds from Argentina during 1994-2010. A total of 5.365 fecal samples from diarrheic calves were screened for BCoV diagnosis by ELISA. The virus was detected in 1.71% (92/5365) of the samples corresponding to 5.95% (63/1058) of the diarrhea cases in 239 beef and 324 dairy farms. The detection rate of BCoV was significantly higher in dairy than in beef herds: 12.13% (29/239) vs. 4.32% (14/324) respectively. Phylogenetic analysis of the hypervariable S1 region of seven representative samples (from different husbandry systems, farm locations and years of sampling) indicated that BCoV strains circulating in Argentinean beef and dairy herds formed a cluster distinct from other geographical regions. Interestingly, Argentinean strains are distantly related (at both the nucleotide and amino acid levels) with the Mebus historic reference BCoV strain included in the vaccines currently available in Argentina. However, Mebus-induced antibodies were capable of neutralizing the BCoV Arg95, a field strain adapted to grow in vitro, and vice versa, indicating that both strains belong to the same CoV serotype reported in cattle. This work represents the first large survey describing BCoV circulation in Argentinean cattle.

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BackgroundIn 2012, equine influenza (EI) virus was confirmed as the cause of outbreaks of respiratory disease in horses throughout South America. In Uruguay and Argentina, hundreds of vaccinated thoroughbred horses in training and racing facilities were clinically affected.ObjectiveTo characterise the EI viruses detected during the outbreak in Uruguay and Argentina.MethodsVirus was detected in nasopharyngeal swabs by a pan‐reactive influenza type A real‐time RT‐PCR. The nucleotide sequence of the HA1 gene was determined and analysed phylogenetically using mega 5 software. Amino acid sequences alignments were constructed and virus was antigenically characterised with specific ferret antisera. Paired serum samples were tested by haemagglutination inhibition and single radial haemolysis.ResultsThe diagnosis of EIV was confirmed by real‐time RT‐PCR, virus isolation and serological testing. The phylogenetic analysis of HA1 gene sequences of 18 EI viruses indicated that all of them belong to clade 1 of the Florida sublineage of the American lineage and are closely related to viruses isolated in the United States in 2012. The HA1 of viruses identified in horses in racing facilities in Maroñas, Uruguay, and in Palermo, Argentina, displayed 100% amino acid sequence identity and were identical to that of a virus isolated in Dubai in 2012, from vaccinated endurance horses recently imported from Uruguay.ConclusionsThe surveillance data reported illustrate the international spread of EI viruses and support the recommendations of the OIE expert surveillance panel to include viruses of the Florida sublineage in vaccines.

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State of latency, well known for several herpesviruses, has been proposed for equine herpesvirus-3 (EHV-3) and supported by epidemiological observations. No detailed assessment about reactivation, patterns of excretion and reexcretion has been formally reported. An experimental reactivation study by corticosteroid treatment in previously naturally infected horses was therefore carried out. Two polo mares with clinical and virologically confirmed history of equine coital exanthema were injected with dexamethasone and prednisolone on 3 successive days. Clinical signs, body temperature and clinical samples for virological and serological studies were obtained daily. Mares did not show any systemic clinical signs or hyperthermia. EHV-3 shedding, seroconversion and the presence of a small lesion were observed in one of the mares under study 2 weeks after corticosteroid treatment. The results demonstrate that this virus exhibits a latency-reactivation behaviour similar to that of other alpha herpesviruses. Reactivation of latency may have an important bearing on the appearance of clinical signs in mares and/or stallions during the breeding season without the actual evidence of transfer from mare to stallion or vice versa.

Equine influenza virus (EIV) causes severe acute respiratory disease in horses. Currently, the strains belonging to the H3N8 subtype are divided into two clades, Florida clade 1 (FC1) and Florida clade 2 (FC2), which emerged in 2002. Both FC1 and FC2 clades were reported in Asian and Middle East countries in the last decade. In this study, we described the evolution, epidemiology, and molecular characteristic of the EIV lineages, with focus on those detected in Asia from 2007 to 2017. The full genome phylogeny showed that FC1 and FC2 constituted separate and divergent lineages, without evidence of reassortment between the clades. While FC1 evolved as a single lineage, FC2 showed a divergent event around 2004 giving rise to two well-supported and coexisting sublineages, European and Asian. Furthermore, two different spread patterns of EIV in Asian countries were identified. The FC1 outbreaks were caused by independent introductions of EIV from the Americas, with the Asian isolates genetically similar to the contemporary American lineages. On the other hand, the FC2 strains detected in Asian mainland countries conformed to an autochthonous monophyletic group with a common ancestor dated in 2006 and showed evidence of an endemic circulation in a local host. Characteristic aminoacidic signature patterns were detected in all viral proteins in both Asian-FC1 and FC2 populations. Several changes were located at the top of the HA1 protein, inside or near antigenic sites. Further studies are needed to assess the potential impact of these antigenic changes in vaccination programs. IMPORTANCE The complex and continuous antigenic evolution of equine influenza viruses (EIVs) remains a major hurdle for vaccine development and the design of effective immunization programs. The present study provides a comprehensive analysis showing the EIV evolutionary dynamics, including the spread and circulation within the Asian continent and its relationship to global EIV populations over a 10-year period. Moreover, we provide a better understanding of EIV molecular evolution in Asian countries and its consequences on the antigenicity. The study underscores the association between the global horse movement and the circulation of EIV in this region. Understanding EIV evolution is imperative in order to mitigate the risk of outbreaks affecting the horse industry and to help with the selection of the viral strains to be included in the formulation of future vaccines.