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In March 2024, highly pathogenic avian influenza virus (HPAIV) clade 2.3.4.4b H5N1 infections were reported in dairy cows in Texas, USA 1 . Rapid dissemination to more than 380 farms in 14 states followed 2 . Here we provide results of two independent clade 2.3.4.4b experimental infection studies evaluating the oronasal susceptibility to and transmission of a US H5N1 bovine isolate, genotype B3.13 (H5N1 B3.13), in calves, and the susceptibility of lactating cows following direct mammary gland inoculation of either H5N1 B3.13 or a current EU H5N1 wild bird isolate, genotype euDG (H5N1 euDG). Inoculation of the calves resulted in moderate nasal replication and shedding with no severe clinical signs or transmission to sentinel calves. In dairy cows, infection resulted in no nasal shedding, but severe acute infection of the mammary gland with necrotizing mastitis and high fever was observed for both H5N1 isolates. Milk production was rapidly and markedly reduced and the physical condition of the cows was severely compromised. Virus titres in milk rapidly peaked at 10 9 50% tissue culture infectious dose (TCID 50 ) per ml, but systemic infection did not ensue. Notably, the adaptive mutation E627K emerged in the viral polymerase basic protein 2 (PB2) after intramammary replication of H5N1 euDG. Our data suggest that in addition to H5N1 B3.13, other HPAIV H5N1 strains have the potential to replicate in the udder of cows and that milk and milking procedures, rather than respiratory spread, are likely to be the primary routes of H5N1 transmission between cattle. Infection studies on highly pathogenic avian influenza virus clade 2.3.4.4b H5N1 on calves and lactating cows indicate that transmission occurs primarily via milk and milking procedures rather than respiratory routes.

Highly pathogenic avian influenza (HPAI) H5N1 haemagglutinin clade 2.3.4.4b was detected in the USA in 2021. These HPAI viruses caused mortality events in poultry, wild birds and wild mammals. On 25 March 2024, HPAI H5N1 clade 2.3.4.4b was confirmed in a dairy cow in Texas in response to a multistate investigation into milk production losses 1 . More than 200 positive herds were identified in 14 US states. The case description included reduced feed intake and rumen motility in lactating cows, decreased milk production and thick yellow milk 2 , 3 . The diagnostic investigation revealed viral RNA in milk and alveolar epithelial degeneration and necrosis and positive immunoreactivity of glandular epithelium in mammary tissue. A single transmission event, probably from birds, was followed by limited local transmission and onward horizontal transmission of H5N1 clade 2.3.4.4b genotype B3.13 (ref.  4 ). Here we sought to experimentally reproduce infection with genotype B3.13 in Holstein yearling heifers and lactating cows. Heifers were inoculated by an aerosol respiratory route and cows by an intramammary route. Clinical disease was mild in heifers, but infection was confirmed by virus detection, lesions and seroconversion. Clinical disease in lactating cows included decreased rumen motility, changes to milk appearance and production losses. Infection was confirmed by high levels of viral RNA detected in milk, virus isolation, lesions in mammary tissue and seroconversion. This study provides the foundation to investigate additional routes of infection, pathogenesis, transmission and intervention strategies. A study describes the experimental infection of cattle with a highly pathogenic avian influenza H5N1 clade 2.3.4.4b genotype B3.13 strain using an aerosol respiratory route for heifers and an intramammary route for lactating cows.

Fecal virus shedding, seroconversion and histopathology were evaluated in 3-7-year-old gnotobiotic calves orally inoculated with porcine deltacoronavirus (PDCoV) (9.0-9.6 log 10 genomic equivalents [GE] of OH-FD22-P5; n =4) or porcine epidemic diarrhea virus (PEDV) (10.2-12.5 log 10 GE of PC21A; n =3). In PDCoV-inoculated calves, an acute but persisting fecal viral RNA shedding and PDCoV-specific serum IgG antibody responses were observed, but without lesions or clinical disease. However, no fecal shedding, seroconversion, histological lesions, and clinical disease were detected in PEDV-inoculated calves. Our data indicate that calves are susceptible to infection by the newly emerged PDCoV, but not by the swine coronavirus, PEDV.

Influenza D virus (IDV) can potentially cause respiratory diseases in livestock. We isolated a new IDV strain from diseased cattle in Japan; this strain is phylogenetically and antigenically distinguished from the previously described IDVs.

Introduction Foot-and-mouth disease (FMD) is a highly contagious viral infection of cloven-hoofed animals that causes substantial economic losses and severe disruptions to agricultural systems globally. It affects animal health and productivity in Nigeria but there is paucity of data across regions and among various animal species. This study determined the seroepidemiology and serotype diversity of the FMD virus (FMDV) among domestic ungulates including cattle, sheep, goats, and pigs, across all geopolitical zones in Nigeria. Materials and methods 1002 sera were collected aseptically from domestic ungulate animals (cattle n  = 511, sheep n  = 182, goat n  = 218 and pigs n  = 91) and were analysed using commercial ELISA kits (ID Vet®, France and IZLER®, Italy) to antibody and serotype-specific antibodies to FMD. Metadata on individual species were collected through questionnaire uploaded on Kobocollect containing sociodemographic data, and distribution of FMD in Nigeria. Results The study revealed an overall FMD seroprevalence of 45.7% for all the various species and regions in Nigeria with specific host prevalence of 69.7% for cattle, 26.9% for sheep, 20.6% for goats, and 8.8% for pigs. Among the 458 FMD-seropositive samples, serotype O was the most predominant (74.9%), followed by A (56.3%), SAT 2 (35.8%), Asia 1 (22.9%) and SAT 1 (16.8%). Kaduna had the highest seroprevalence (88.9%), while Cross River had the lowest (9.1%). Multi-serotype infections were most common in cattle (32%). Health status and body condition were major determinants of susceptibility, with unhealthy animals being five times more likely to test positive for FMD (OR = 5.479, p  < 0.001). While cattle constituted the majority of samples analysed, the inclusion of sheep, goats, and pigs provided comparative insights into interspecies variation in exposure and serotype occurrence. Conclusion We have systematically determined FMDV seroprevalence and serotype distribution in various domestic ungulate species across all the geopolitical zones in Nigeria. Our findings reveal that serotype O and A remain dominant across Nigeria, while the unexpected detection of serotype Asia 1 indicates possible viral evolution or introduction from new sources. Furthermore, border proximity was not a significant predictor of infection, suggesting localized transmission dynamics. These insights underscore the need for improved surveillance, context-specific multivalent vaccination strategies, and further molecular investigation of emerging serotypes in Nigeria.

Bovine coronavirus (BCoV) and SARS-CoV-2, both belonging to the Betacoronavirus genus, are major pathogens affecting cattle and humans, respectively. BCoV causes respiratory and enteric diseases in cattle, leading to significant economic losses, while the detection of SARS-CoV-2 in various animal species raises concerns about interspecies transmission. This study assessed the seroprevalence of both viruses in cattle and buffaloes from southern Italy, considering species and regional origin as potential risk factors. Among 945 animals analyzed (491 cattle, 454 buffaloes), 435 (46%) tested positive for BCoV and 27 (2.8%) for SARS-CoV-2. Significant differences were observed between species and regions (BCoV: p  < 0.0001; SARS-CoV-2: p  = 0.0029). Among BCoV-positive samples, 67.1% of cattle but no buffaloes showed neutralizing antibodies ( p  = 0.0006). Twelve SARS-CoV-2-positive cattle were also BCoV-positive. However, the observed SARS-CoV-2 ELISA reactivity cannot be conclusively interpreted as confirmed SARS-CoV-2 exposure and does not allow discrimination between true exposure and non-specific serological reactivity. Longitudinal and molecular studies are needed to further clarify infection dynamics and possible antibody cross-reactivity among Betacoronaviruses.

Bovine Respiratory Disease (BRD) is the leading cause of mortality in calves. The objective of this study was to examine the response of the host’s bronchial lymph node transcriptome to Bovine Respiratory Syncytial Virus (BRSV) in a controlled viral challenge. Holstein-Friesian calves were either inoculated with virus (10 3.5 TCID 50 /ml × 15 ml) (n = 12) or mock challenged with phosphate buffered saline (n = 6). Clinical signs were scored daily and blood was collected for haematology counts, until euthanasia at day 7 post-challenge. RNA was extracted and sequenced (75 bp paired-end) from bronchial lymph nodes. Sequence reads were aligned to the UMD3.1 bovine reference genome and differential gene expression analysis was performed using EdgeR. There was a clear separation between BRSV challenged and control calves based on gene expression changes, despite an observed mild clinical manifestation of the disease. Therefore, measuring host gene expression levels may be beneficial for the diagnosis of subclinical BRD. There were 934 differentially expressed genes (DEG) (p < 0.05, FDR <0.1, fold change >2) between the BRSV challenged and control calves. Over-represented gene ontology terms, pathways and molecular functions, among the DEG, were associated with immune responses. The top enriched pathways included interferon signaling, granzyme B signaling and pathogen pattern recognition receptors, which are responsible for the cytotoxic responses necessary to eliminate the virus.

The highly pathogenic avian influenza virus (HPAIV) H5N1, first isolated in 1996 in China, spread rapidly across Eurasia and caused major epizootics in wild and domesticated birds, as well as spillover infections in humans characterised by high mortality. Avian influenza viruses are therefore candidate viruses for a human pandemic. Surprisingly, HPAIV was not isolated in North America until 2014. With the help of intensive biological sampling and viral genome sequencing, the intrusion of HPAIV into North America could be retraced to two separate events. First, migratory birds carried HPAIV from East Siberia via Beringia and dispersed the virus along the Pacific flyway. After reassortment with genes of local low pathogenic avian influenza viruses, HPAIV H5 caused 2015 a major epizootic on poultry farms in the US Mid‐West. After costly containment, HPAIV dropped below the detection limit. In 2021, Eurasian HPAIV H5 viruses arrived a second time in North America, carried by migratory birds to Canada via the Atlantic flyway, using Iceland as a stop. The H5 virus then spread with water birds along the East Coast of the United States and dispersed across the United States. In contrast to the 2015 poultry outbreak, spillover infections into diverse species of mammals were now observed. The events culminated in the 2024 HPAIV H5 epizootic in dairy cows affecting 300 dairy herds in 14 US states. The cattle epizootic was spread mainly by milking machinery and animal transport. On affected farms infected cats developed fatal neurological diseases. Retail milk across the United States frequently contains viral RNA, but so far only a few milk farm workers have developed mild symptoms. The tracing of HPAIV with viral genome sequencing complicated the taxonomical naming of influenza viruses raising fundamental problems in how to mirror biological complexity in written plain language, rendering communication with the lay public difficult. With the help of intensive biological sampling and viral gene sequencing, the intrusion of high pathogenicity avian influenza viruses (HPAIV) into North America could be retraced. After reassortment with genes of local low pathogenic avian influenza viruses, HPAIV H5 caused in 2015 a major epizootic on poultry farms in the US Mid‐West and in 2024 an epizootic in dairy cows affecting 300 dairy herds in 14 US states. Figure credit: Hu et al. (2024).

A viral metagenomics approach was used to investigate fecal samples of Japanese calves with and without diarrhea. Of the different viral pathogens detected, read counts gave nearly complete astrovirus-related RNA sequences in 15 of the 146 fecal samples collected in three distinct areas (Hokkaido, Ishikawa, and Kagoshima Prefectures) between 2009 and 2015. Due to the lack of genetic information about bovine astroviruses (BoAstVs) in Japan, these sequences were analyzed in this study. Nine of the 15 Japanese BoAstVs were closely related to Chinese BoAstVs and clustered into a lineage (tentatively named lineage 1) in all phylogenetic trees. Three of 15 strains were phylogenetically separate from lineage 1, showing low sequence identities, and clustered instead with an American strain isolated from cattle with respiratory disease (tentatively named lineage 2). Interestingly, two of 15 strains clustered with lineage 1 in the open reading frame (ORF)1a and ORF1b regions, while they clustered with lineage 2 in the ORF2 region. Remarkably, one of 15 strains exhibited low amino acid sequence similarity to other BoAstVs and was clustered separately with porcine astrovirus type 5 in all trees, and ovine astrovirus in the ORF2 region, suggesting past interspecies transmission.

Calf diarrhea is one of the common diseases involved in the process of calf feeding. In this study, a sample of calf diarrhea that tested positive for bovine coronavirus and bovine astrovirus was subjected to high-throughput sequencing. The reassembly revealed the complete genomes of bovine norovirus, bovine astrovirus, bovine kobuvirus, and the S gene of bovine coronavirus. Phylogenetic analysis showed that the ORF2 region of bovine astrovirus had the lowest similarity with other strains and gathered in the Mamastrovirus unclassified genogroup, suggesting a new serotype/genotype could appear. Compared with the most closely related strain, there are six amino acid mutation sites in the S gene of bovine coronavirus, most of which are located in the S1 subunit region. The bovine norovirus identified in our study was BNoV-GIII 2, based on the VP1 sequences. The bovine kobuvirus is distributed in the Aichi virus B genus; the P1 gene shows as highly variable, while the 3D gene is highly conserved. These findings enriched our knowledge of the viruses in the role of calf diarrhea, and help to develop an effective strategy for disease prevention and control.