Description of the outbreak of equine influenza (H3N8) in the United Kingdom in 2003, during which recently vaccinated horses in Newmarket developed respiratory disease

Adaptation potential of H3N8 canine influenza virus in human respiratory cells

In 2004, the equine-origin H3N8 canine influenza virus (CIV) first caused an outbreak with lethal cases in racing greyhounds in Florida, USA, and then spread to domestic dogs nationwide. Although transmission of this canine virus to humans has not been reported, it is important to evaluate its zoonotic potential because of the high contact opportunities between companion dogs and humans. To gain insight into the interspecies transmissibility of H3N8 CIV, we tested its adaptability to human respiratory A549 cells through successive passages. We found that CIV acquired high growth properties in these cells mainly through mutations in surface glycoproteins, such as hemagglutinin (HA) and neuraminidase (NA). Our reverse genetics approach revealed that HA2-K82E, HA2-R163K, and NA-S18L mutations were responsible for the increased growth of CIV in human cells. Molecular analyses revealed that both HA2 mutations altered the optimum pH for HA membrane fusion activity and that the NA mutation changed the HA-NA functional balance. These findings suggest that H3N8 CIV could evolve into a human pathogen with pandemic potential through a small number of mutations, thereby posing a threat to public health in the future.

A Cold Case of Equine Influenza Disentangled with Nanopore Sequencing

Massive sequencing techniques have allowed us to develop straightforward approaches for the whole genome sequencing of viruses, including influenza viruses, generating information that is useful for improving the levels and dimensions of data analysis, even for archival samples. Using the Nanopore platform, we determined the whole genome sequence of an H3N8 equine influenza virus, identified from a 2005 outbreak in Apulia, Italy, whose origin had remained epidemiologically unexplained. The virus was tightly related (>99% at the nucleotide level) in all the genome segments to viruses identified in Poland in 2005–2008 and it was seemingly introduced locally with horse trading for the meat industry. In the phylogenetic analysis based on the eight genome segments, strain ITA/2005/horse/Bari was found to cluster with sub-lineage Florida 2 in the HA and M genes, whilst in the other genes it clustered with strains of the Eurasian lineage, revealing a multi-reassortant nature.

An epidemiological overview of the equine influenza epidemic in Great Britain during 2019

BACKGROUND

During 2019, an epidemic of equine influenza (EI) occurred in Europe.

OBJECTIVES

To describe the epidemiology of the 2019 EI epidemic within Great Britain (GB).

STUDY DESIGN

Retrospective descriptive study of laboratory confirmed EI cases.

METHODS

Epidemiological data were obtained from veterinary surgeons referring samples for EI virus testing. Where available, data on confirmed cases and their wider resident population on EI-infected premises were collated and described. On a national level, spatial and temporal representations, consisting of choropleth maps and epidemic curves, described the spread of EI. EI-infected premises-level factors associated with the first of two epidemic phases were investigated using ordinary logistic regression analysis.

RESULTS

There were 412 confirmed cases and 234 EI-infected premises, with the first of two epidemic phases occurring between January and April, followed by a second phase through to August. The median age of confirmed cases was 5 years and Sports horses (24%) and Cobs (16%) made up the highest proportions by general horse type and breed. Among confirmed cases 72% were unvaccinated and 18% were vaccinated against EI. New horses arriving within 2 weeks of a confirmed case were reported by 42% of EI-infected premises. Investigation of EI-infected premises biosecurity measures indicated that 23% quarantined new arrivals, 37% had isolation facilities and 57% of resident horses were vaccinated. EI-infected premises were more likely in the first than second epidemic phase to be classified as professional, have a vaccinated confirmed case and EI confirmed in a newly arrived animal.

MAIN LIMITATIONS

Data were collected at a single time point for each EI-infected premises with no follow ups performed.

CONCLUSIONS

During 2019, EI-infected premises generally had low levels of population vaccine coverage and implemented limited preventive biosecurity measures, particularly linked to horse movements. Without substantial improvements in infectious disease prevention and control, the GB equine population remains at risk of future EI epidemics.

Frequency of Detection and Prevalence Factors Associated with Common Respiratory Pathogens in Equids with Acute Onset of Fever and/or Respiratory Signs (2008–2021)

A voluntary biosurveillance program was established in 2008 in order to determine the shedding frequency and prevalence factors for common respiratory pathogens associated with acute onset of fever and/or respiratory signs in equids from the USA. Over a period of 13 years, a total of 10,296 equids were enrolled in the program and nasal secretions were analyzed for the qPCR detection of equine influenza virus (EIV), equine herpesvirus-1 (EHV-1), EHV-4, equine rhinitis A and B virus (ERVs), and Streptococcus equi subspecies equi (S. equi). Single infections with respiratory pathogens were detected in 21.1% of the submissions with EIV (6.8%) and EHV-4 (6.6%) as the two most prevalent viruses, followed by S. equi (4.7%), ERVs (2.3%), and EHV-1 (0.7%). Multiple pathogens were detected in 274 horses (2.7%) and no respiratory pathogens in 7836 horses (76.2%). Specific prevalence factors were determined for each of the six respiratory pathogen groups; most differences were associated with age, breed, and use of the horses, while the clinical signs were fairly consistent between viral and bacterial respiratory infections. Monitoring the frequency of detection of common respiratory pathogens is important in order to gain a better understanding of their epidemiology and to implement management practices aimed at controlling disease spread.

A Review on Equine Influenza from a Human Influenza Perspective

Influenza A viruses (IAVs) have a main natural reservoir in wild birds. IAVs are highly contagious, continually evolve, and have a wide host range that includes various mammalian species including horses, pigs, and humans. Furthering our understanding of host-pathogen interactions and cross-species transmissions is therefore essential. This review focuses on what is known regarding equine influenza virus (EIV) virology, pathogenesis, immune responses, clinical aspects, epidemiology (including factors contributing to local, national, and international transmission), surveillance, and preventive measures such as vaccines. We compare EIV and human influenza viruses and discuss parallels that can be drawn between them. We highlight differences in evolutionary rates between EIV and human IAVs, their impact on antigenic drift, and vaccine strain updates. We also describe the approaches used for the control of equine influenza (EI), which originated from those used in the human field, including surveillance networks and virological analysis methods. Finally, as vaccination in both species remains the cornerstone of disease mitigation, vaccine technologies and vaccination strategies against influenza in horses and humans are compared and discussed.

Equine Influenza

Horses are the third major mammalian species, along with humans and swine, long known to be subject to acute upper respiratory disease from influenza A virus infection. The viruses responsible are subtype H7N7, which is believed extinct, and H3N8, which circulates worldwide. The equine influenza lineages are clearly divergent from avian influenza lineages of the same subtypes. Their genetic evolution and potential for interspecies transmission, as well as clinical features and epidemiology, are discussed. Equine influenza is spread internationally and vaccination is central to control efforts. The current mechanism of international surveillance and virus strain recommendations for vaccines is described.

High prevalence of Mycoplasma equirhinis in Thoroughbred horses with respiratory symptoms in autumn 2018

Mycoplasma species are often isolated from horses with respiratory symptoms; however, the pathogenicity of Mycoplasma is still unclear. In autumn of 2018, we encountered an increase in cases with respiratory symptoms, mainly coughing, in a group of Thoroughbred racehorses in Japan. We examined tracheal wash samples obtained from 40 of those cases. Bacteria and viruses that commonly cause respiratory symptoms were investigated, and anaerobes were detected in only 5 cases and Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) was detected in only 1 case of 40 cases with loop-mediated isothermal amplification assay. S. zooepidemicus and Streptococcus pneumoniae were isolated at a bacterial count of higher than 1.0 × 10⁴ CFU/ml from 5 and 2 cases of 28 cases cultured, respectively. None of the viruses investigated was detected in 40 cases. Mycoplasma equirhinis (M. equirhinis) was isolated from 40.0% (16/40) of the cases, which was higher than previously reported isolation rates. The rate of M. equirhinis isolation in the cases from 2018 was significantly higher than the isolation rates in the other horses: clinical cases with respiratory symptoms in 2019-2020 (13.6%, 3/22) and healthy horses (13.5%, 5/37) in Japan. In this study, the isolation rate of M. equirhinis from horse group with cough symptoms in 2018 was high and no other common etiological agents were detected. The pathogenesis of M. equirhinis is still unclear, however, M. equirhinis might have been associated with respiratory symptoms in the Thoroughbred horse cases in 2018.

Global epidemiology of Equine Influenza viruses; "A possible emerging zoonotic threat in future" an extensive systematic review with evidence

There are different opinions around the World regarding the zoonotic capability of H3N8 equine influenza viruses. In this report, we have tried to summarize the findings of different research and review articles from Chinese, English, and Mongolian Scientific Literature reporting the evidence for equine influenza virus infections in human beings. Different search engines i.e. CNKI, PubMed, ProQuest, Chongqing Database, Mongol Med, and Web of Knowledge yielded 926 articles, of which 32 articles met the inclusion criteria for this review. Analyzing the epidemiological and Phylogenetic data from these articles, we found a considerable experimental and observational evidence of H3N8 equine influenza viruses infecting human being in different parts of the World in the past. Recently published articles from Pakistan and China have highlighted the emerging threat and capability of equine influenza viruses for an epidemic in human beings in future. In this review article we have summarized the salient scientific reports published on the epidemiology of equine influenza viruses and their zoonotic aspect. Additionally, several recent developments in the start of 21st century, including the transmission and establishment of equine influenza viruses in different animal species i.e. camels and dogs, and presumed encephalopathy associated to influenza viruses in horses, have documented the unpredictable nature of equine influenza viruses. In sum up, several reports has highlighted the unpredictable nature of H3N8 EIVs highlighting the need of continuous surveillance for H3N8 in equines and humans in contact with them for novel and threatening mutations.

Genome-informed characterisation of antigenic drift in the haemagglutinin gene of equine influenza strains circulating in the United States from 2012 to 2017

Equine influenza virus (EIV) is a major infectious pathogen causing significant respiratory signs in equids worldwide. Voluntary surveillances in the United States recently reported EIV detection in horses with respiratory signs even with adequate vaccine protocols and biosecurity programs and posed a concern about suboptimal effectiveness of EIV vaccine in the United States. This study aims to determine the genetic characteristics of 58 field EIV H3N8 strains in the United States from 2012 to 2017 using the phylogenetic analysis based on the haemagglutinin (HA) gene. Amino acid substitution and acquisition of N-glycosylation of the HA gene were also evaluated. Phylogenetic analysis identified that almost all US field strains belonged to the Florida clade 1 (FC1) except one Florida clade 2 strain from a horse imported in 2014. US EIV strains in 2017 shared 11 fixed amino acid substitutions in the HA gene, compared to the vaccine strain (A/equine/Ohio/2003), and two additional amino acid substitutions were detected in 2019. The introduction of foreign EIV strains into the United States was not detected, but antigenic drift without acquisition of N-glycosylation in the HA gene was observed in US field strains until 2017. Considering the global dominance of FC1 strains, subsequent antigenic drift of US EIV strains should be monitored for better effectiveness of the EIV vaccine in the United States and global equine industries.

Equine influenza: a comprehensive review from etiology to treatment

Influenza is an extremely contagious respiratory disease, which predominantly affects the upper respiratory tract. There are four types of influenza virus, and pigs and chickens are considered two key reservoirs of this virus. Equine influenza (EI) virus was first identified in horses in 1956, in Prague. The influenza A viruses responsible for EI are H7N7 and H3N8. Outbreaks of EI are characterized by their visible and rapid spread, and it has been possible to isolate and characterize H3N8 outbreaks in several countries. The clinical diagnosis of this disease is based on the clinical signs presented by the infected animals, which can be confirmed by performing complementary diagnostic tests. In the diagnosis of EI, in the field, rapid antigen detection tests can be used for a first approach. Treatment is based on the management of the disease and rest for the animal. Regarding the prognosis, it will depend on several factors, such as the animal's vaccination status. One of the important points in this disease is its prevention, which can be done through vaccination. In addition to decreasing the severity of clinical signs and morbidity during outbreaks, vaccination ensures immunity for the animals, reducing the economic impact of this disease.

Determining Equine Influenza Virus Vaccine Efficacy-The Specific Contribution of Strain Versus Other Vaccine Attributes

Vaccination is an effective tool to limit equine influenza virus (EIV H3N8) infection, a contagious respiratory disease with potentially huge economic impact. The study assessed the effects of antigenic change on vaccine efficacy and the need for strain update. Horses were vaccinated (V1 and V2) with an ISCOMatrix-adjuvanted, whole inactivated virus vaccine (Equilis Prequenza, group 2, FC1 and European strains) or a carbomer-adjuvanted, modified vector vaccine (ProteqFlu, group 3, FC1 and FC2 HA genes). Serology (SRH, HI, VN), clinical signs and viral shedding were assessed in comparison to unvaccinated control horses. The hypothesis was that group 2 (no FC2 vaccine strain) would be less well protected than group 3 following experimental infection with a recent FC2 field strain (A/equi-2/Wexford/14) 4.5 months after vaccination. All vaccinated horses had antibody titres to FC1 and FC2. After challenge, serology increased more markedly in group 3 than in group 2. Vaccinated horses had significantly lower total clinical scores and viral shedding. Unexpectedly, viral RNA shedding was significantly lower in group 2 than in group 3. Vaccination induced protective antibody titres to FC1 and FC2 and reduced clinical signs and viral shedding. The two tested vaccines provided equivalent protection against a recent FC2 EIV field strain.

Fatal multiple outbreaks of equine influenza H3N8 in Nigeria, 2019: The first introduction of Florida clade 1 to West Africa

In December 2018, suspected outbreaks of equine influenza (EI) were observed in donkeys in Sokoto State, in the extreme northwest of Nigeria bordering the Republic of the Niger. Equine influenza virus (EIV) subtype H3N8 was the etiologic agent identified in the outbreaks using real-time RT-qPCR and sequencing of both the partial haemagglutinin (HA) gene and the complete genome. Since then the H3N8 virus spread to 7 of the 19 northern states of Nigeria, where it affected both donkeys and horses. Phylogenetic analysis of the partial and complete HA gene revealed the closest nucleotide similarity (99.7%) with EIVs belonging to the Florida clade 1 (Fc-1) of the American lineage isolated in 2018 from Argentina and Chile. In total, 80 amino acid substitutions were observed in the viral proteins when compared to the OIE-recommended Fc-1 vaccine strains. The HA and neuraminidase proteins respectively had 13 and 16 amino acid substitutions. This study represents the first reported outbreak of EI caused by an Fc-1 virus in Nigeria and in the West Africa sub-region. Based on this report, extensive disease surveillance in equids is required to establish the circulating lineages and design an effective control strategy to protect the considerable population of horses and donkeys in the country.

Antibody Responses Against Equine Influenza Virus Induced by Concurrent and by Consecutive Use of an Inactivated Equine Influenza Virus Vaccine and a Modified Live Equine Herpesvirus Type 1 Vaccine in Thoroughbred Racehorses

An inactivated equine influenza virus (EIV) vaccine and a live equine herpesvirus type 1 (EHV-1) vaccine are usually administered concurrently to Thoroughbred racehorses in Japan. The objective of this study was to evaluate whether concurrent administration of an inactivated EIV vaccine and a live EHV-1 vaccine in Thoroughbred racehorses influences the antibody response against EIV. We compared the antibody response against EIV in horses administered both vaccines on the same day (Group A; n = 27) and the response in horses administered an inactivated EIV vaccine first and then a live EHV-1 vaccine 1-2 weeks later (Group B; n = 20). In both groups, geometric mean hemagglutination inhibition (HI) titers against A/equine/Ibaraki/1/2007 and A/equine/Yokohama/aq13/2010 increased significantly after EIV vaccination. However, the percentage of horses that showed a twofold increase or greater in HI titers against A/equine/Yokohama/aq13/2010 was significantly higher in Group B (75%) than in Group A (37%; P = .02). These results suggest that the concurrent use of an inactivated EIV vaccine and a live EHV-1 vaccine reduced the immune response against EIV to some extent, and it would be better to use these vaccines consecutively, especially for naïve horses or horses whose vaccination history is incomplete.

Conflict Between Direct Experience and Research-Based Evidence Is a Key Challenge to Evidence-Based Respiratory Medicine on British Racing Yards

Inflammatory airway disease (IAD) is a commonly diagnosed but variably defined syndrome of equine lower airway inflammation. The most recent American College of Veterinary Internal Medicine (ACVIM) consensus statement, informed by research evidence, recommends a case definition based on clinical signs (poor performance or occasional coughing of at least 3 weeks duration), increased endoscopically-visible tracheal mucus, and bronchoalveolar lavage cytology, and proposes that the condition should be termed ‘mild-moderate equine asthma' (mEA). In British Thoroughbred racehorses, research to date has focused on airway inflammation defined by increased tracheal mucus and inflammatory tracheal wash sample cytology. It has been unclear whether or to what extent the ACVIM consensus statement has influenced the practice of British racing veterinarians. The aim of this qualitative study was to characterize and understand rationales for current practices relating to diagnosing and managing airway inflammation in British racehorses. Audio-recorded focus group discussions were conducted with 25 participants from four veterinary practices in England. Practices were purposively selected to represent those responsible for different types of racehorse, in different geographical regions. Thematic analysis of transcripts identified (i) an over-arching theme of serving the racing industry within which two further themes (ii) disregarding of the consensus and (iii) the pragmatic clinician were nested. The requirement to serve the racing industry was a key driver of clinical approaches, strongly influenced in particular by the trainer. Participants widely disregarded the consensus case definition of IAD/mEA for British racehorses because of perceived differences in etiology, perceived lack of practicability, particularly of BAL sampling, and perceived lack of understanding of the British racing context by consensus authors. Participants shared a strong professional identity as pragmatic clinicians providing an individualized clinical approach based on direct experience, which was often prioritized as the most valuable evidence with which to inform clinical decision-making. Lack of alignment with international consensus presents a barrier to practicing and furthering evidence-based medicine. Improved dialogue and partnership in research would be valuable and further research tailored for this population, including continuing development of contextually acceptable diagnostic methods, may be required.

Equine influenza vaccination as reported by horse owners and factors influencing their decision to vaccinate or not

BACKGROUND

Equine influenza virus is a highly contagious respiratory pathogen that causes pyrexia, anorexia, lethargy and coughing in immunologically naïve horses. Vaccines against equine influenza are available and vaccination is mandatory for horses that participate in affiliated competitions, but this group forms a small proportion of the total horse population. The aims of this study were to: i) identify the equine influenza vaccination rate as reported in 2016 by horse owners in the United Kingdom (UK); ii) examine the demographics of owners and horses which were associated with significantly lower influenza vaccination rates and iii) explore factors that influence horse owners' decisions around influenza vaccine uptake.

RESULTS

Responses from 4837 UK horse owners who were responsible for 10,501 horses were analysed. An overall equine influenza vaccination rate of 80% (8385/10501) was reported. Several owner demographic characteristics were associated with significantly lower (p<0.05) reported equine influenza vaccination rates including: some geographical locations, increasing horse owner age, annual household income of less that £15,000 and owning more than one horse. Horse-related features which were associated with significantly lower reported equine influenza vaccination rates included age ranges of <4 years and > 20 years, use as a companion or breeding animal or leaving their home premises either never or at most once a year. The most common reasons cited for failing to vaccinate horses was no competition activity, lack of exposure to influenza and expense of vaccines. In contrast, the most common underlying reasons given by horse owners who vaccinated their horse were protection of the individual horse against disease, veterinary advice and to protect the national herd. Owners of vaccinated horses had less previous experience of an influenza outbreak or adverse reaction to vaccination compared with owners of unvaccinated horses.

CONCLUSIONS

This study documented a high rate of equine influenza vaccination as reported by owners in a substantial number of horses in the UK, but this does not reflect the level of protection. Sub-populations of horses which were less likely to be vaccinated and the factors that influence each owner's decision around vaccination of their horses against equine influenza were identified, but may alter following the 2019 European influenza outbreak. This information may nevertheless help veterinary surgeons identify "at-risk" patients and communicate more personalised advice to their horse-owning clients. It may also influence educational campaigns about equine influenza directed to horse owners, which aim to improve uptake of vaccination against this pathogen.

Annual booster vaccination and the risk of equine influenza to Thoroughbred racehorses

BACKGROUND

Equine influenza (EI) outbreaks occurred among horses on four racing yards (two National Hunt, one Flat, one mixed National Hunt racing/breeding yard) in Ireland within a 4-week period.

OBJECTIVES

To carry out a detailed analysis of racing yards affected in order to identify the source of infection and monitor virus spread among a vaccinated population.

STUDY DESIGN

Observational field study.

METHODS

Epidemiological and vaccination data along with repeat clinical samples were collected from 118 horses on four premises.

RESULTS

Failure to implement appropriate biosecurity measures following the introduction of new arrivals and the return of horses from equestrian events contributed to disease spread as did the movement of horses within premises. Mixing of racing and non-racing populations with inadequate vaccination histories also facilitated virus transmission. The index case(s) on all premises was vaccinated in accordance with the Turf Club rules. Vaccine breakdown was observed across all products in 27/80 horses (33.8%) with an up-to-date vaccination record. Eighteen of the 27 (66.7%) horses had not received a booster vaccination within the previous 6 months and 10 (37%) horses were due annual booster vaccination at the time of developing clinical signs.

MAIN LIMITATIONS

The interpretation of laboratory results followed a delay in veterinary intervention.

CONCLUSIONS

Annual booster vaccination should not be relied on as the sole preventative measure against EI. The findings of this study suggest that increasing the frequency of booster vaccinations may be beneficial particularly in young horses and that synchronised scheduling of vaccination regimes across racing yards may contribute to high-risk periods for EI virus (EIV) transmission.

Equine Influenza Serological Methods

Serologic tests for equine influenza virus (EIV) antibodies are used for many purposes, including retrospective diagnosis, subtyping of virus isolates, antigenic comparison of different virus strains, and measurement of immune responses to EIV vaccines. The hemagglutination inhibition (HI) assay, single radial hemolysis (SRH), and serum micro-neutralization tests are the most widely used for these purposes and are described here. The presence of inhibitors of hemagglutination in equine serum complicates interpretation of HI assay results, and there are alternative protocols (receptor-destroying enzyme, periodate, trypsin-periodate) for their removal. With the EIV H3N8 strains in particular, equine antibody titers may be magnified by pre-treating the HI test antigen with Tween-80 and ether. The SRH assay offers stronger correlations between serum antibody titers and protection from disease. Other tests are sometimes used for specialized purposes such as the neuraminidase-inhibition assay for subtyping, or ELISA for measuring different specific antibody isotypes, and are not described here.

Host-range shift of H3N8 canine influenza virus: a phylodynamic analysis of its origin and adaptation from equine to canine host

Prior to the emergence of H3N8 canine influenza virus (CIV) and the latest avian-origin H3N2 CIV, there was no evidence of a circulating canine-specific influenza virus. Molecular and epidemiological evidence suggest that H3N8 CIV emerged from H3N8 equine influenza virus (EIV). This host-range shift of EIV from equine to canine hosts and its subsequent establishment as an enzootic CIV is unique because this host-range shift was from one mammalian host to another. To further understand this host-range shift, we conducted a comprehensive phylodynamic analysis using all the available whole-genome sequences of H3N8 CIV. We found that (1) the emergence of H3N8 CIV from H3N8 EIV occurred in approximately 2002; (2) this interspecies transmission was by a reassortant virus of the circulating Florida-1 clade H3N8 EIV; (3) once in the canine species, H3N8 CIV spread efficiently and remained an enzootic virus; (4) H3N8 CIV evolved and diverged into multiple clades or sublineages, with intra and inter-lineage reassortment. Our results provide a framework to understand the molecular basis of host-range shifts of influenza viruses and that dogs are potential “mixing vessels” for the establishment of novel influenza viruses.

Equine Rhinitis A Virus Infection in Thoroughbred Racehorses-A Putative Role in Poor Performance?

The aim of this study was to identify respiratory viruses circulating amongst elite racehorses in a training yard by serological testing of serial samples and to determine their impact on health status and ability to race. A six-month longitudinal study was conducted in 30 Thoroughbred racehorses (21 two-year-olds, five three-year-olds and four four-year-olds) during the Flat racing season. Sera were tested for the presence of antibodies against equine herpesvirus 1 and 4 (EHV-1 and EHV-4) and equine rhinitis viruses A and B (ERAV and ERBV) by complement fixation (CF) and equine arteritis virus (EAV) by ELISA. Antibodies against equine influenza (EI) were measured by haemagglutination inhibition (HI). Only ERAV was circulating in the yard throughout the six-month study period. Seroconversion to ERAV frequently correlated with clinical respiratory disease and was significantly associated with subsequent failure to race (p = 0.0009). Over 55% of the two-year-olds in the study seroconverted to ERAV in May and June. In contrast, only one seroconversion to ERAV was observed in the older horses. They remained free of any signs of respiratory disease and raced successfully throughout the study period. The importance of ERAV as a contributory factor in the interruption of training programmes for young horses may be underestimated.

An economic analysis of a contingency model utilising vaccination for the control of equine influenza in a non-endemic country

Background

Equine influenza (EI) is an infectious respiratory disease of horses that has never been reported in New Zealand (NZ). However, the 2007 EI outbreak in Australia, previously EI free, spurred the NZ government and stakeholders into evaluating alternative EI control strategies in order to economically justify any future decision to eradicate or manage EI. To build on the policy debate, this paper presents an epinomic (epidemiologic and economic) modelling approach to evaluate alternative control strategies. An epidemiologic model to determine how alternative EI control strategies influence the distribution of EI. Model results were then input into a cost-benefit analysis framework, to identify the return and feasibility of alternative EI eradication strategies in NZ.

Methods

The article explores nine alternative eradication scenarios and two baseline strategies. The alternative scenarios consisted of three vaccination strategies (suppressive, protective or targeted) starting at three time points to reflect the commercial breeding-cycle. These alternatives were compared to two breeding-cycle adjusted baselines: movement restriction in the breeding season (August to January) or non-breeding season (February to July). The economic loss parameters were incursion response, impact to the commercial racing industry (breeding, sales and racing), horse morbidity and mortality, and compensation to industry participants.

Results and conclusions

Results suggest that the economic viability of the EI eradication programme is dependent on when within the breeding-cycle the EI outbreak occurs. If an outbreak were to occur, the return on each dollar invested for protective or suppressive vaccination strategies would be between NZD$3.67 to NZD$4.89 and between NZD$3.08 to NZD$3.50 in the breeding and non-breeding seasons, respectively. Therefore, protective or suppressive vaccination strategies could be prioritised, regardless of season. As multiple industry stakeholders benefit from these strategies, the study will enable policy development and to better formulate a user-pays eradication programme.

RETRACTED: An epidemiological investigation of associated risk factors with equine influenza (H3N8) epidemic 2015-16 in Pakistan

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the Editors-in-Chief. The article duplicates significant parts of a paper that had already appeared in Preventative Veterinary Medicine, 149, 132-139; https://doi.org/10.1016/j.prevetmed.2017.12.005. One of the conditions of submission of a paper for publication is that authors declare explicitly that the paper has not been previously published and is not under consideration for publication elsewhere. Re-use of any data should be appropriately cited. As such this article represents a misuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.

Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey

BACKGROUND

In 2013, there was an outbreak of acute respiratory disease in racehorses in Turkey. The clinical signs were consistent with equine influenza (EI).

OBJECTIVE

The aim was to confirm the cause of the outbreak and characterise the causal virus.

METHODS

A pan-reactive influenza type A real-time RT-PCR and a rapid antigen detection kit were used for confirmatory diagnosis of equine influenza virus (EIV). Immunological susceptibility to EIV was examined using single radial haemolysis and ELISA. Antigenic characterisation was completed by haemagglutinin inhibition using a panel of specific ferret antisera. Genetic characterisation was achieved by whole-genome sequencing using segment-specific primers with M13 tags.

RESULTS

A H3N8 EIV of the Florida clade 2 sublineage (FC2) was confirmed as the causal agent. The index cases were unvaccinated and immunologically susceptible. Phylogenetic analysis of the HA1 and NA genes demonstrated that A/equine/Ankara/1/2013 clustered with the FC2 strains circulating in Europe. Antigenic characterisation confirmed the FC2 classification and demonstrated the absence of significant drift. Whole-genome sequencing indicated that A/equine/Ankara/1/2013 is most closely related to the viruses described as the 179 group based on the substitution I179V in HA1, for example A/equine/East Renfrewshire/2/2011, A/equine/Cambremer/1/2012 and A/equine/Saone et Loire/1/2015. The greatest diversity was observed in the NS1 segment and the polymerase complex.

CONCLUSIONS

The first recorded outbreak of EI in Turkey was caused by an FC2 virus closely related to viruses circulating in Europe. Antigenic and genetic characterisation gave no indication that the current OIE recommendations for EI vaccine composition require modification.

Multifocal Equine Influenza Outbreak with Vaccination Breakdown in Thoroughbred Racehorses

Equine influenza (EI) outbreaks occurred on 19 premises in Ireland during 2014. Disease affected thoroughbred (TB) and non-TB horses/ponies on a variety of premises including four racing yards. Initial clinical signs presented on 16 premises within a two-month period. Extensive field investigations were undertaken, and the diagnostic effectiveness of a TaqMan RT-PCR assay was demonstrated in regularly-vaccinated and sub-clinically-affected horses. Epidemiological data and repeat clinical samples were collected from 305 horses, of which 40% were reported as clinically affected, 39% were identified as confirmed cases and 11% were sub-clinically affected. Multivariable analysis demonstrated a significant association between clinical signs and age, vaccination status and number of vaccine doses received. Vaccine breakdown was identified in 31% of horses with up to date vaccination records. This included 27 horses in four different racing yards. Genetic and antigenic analysis identified causal viruses as belonging to Clade 2 of the Florida sublineage (FCL2). At the time of this study, no commercially available EI vaccine in Ireland had been updated in line with World Organisation for Animal Health (OIE) recommendations to include a FCL2 virus. The findings of this study highlight the potential ease with which EI can spread among partially immune equine populations.

Investigating the epidemiology of EI epidemic spread in the Province of Khyber Pakhtunkhwa, Pakistan in 2015-16

EI in non-vaccinated population causes disruption and economic losses. To identify the risk factors associated with the EI epidemics in equids in Pakistan, a 1:1 matched case control study was conducted during 2015-2016. Including a total of 197 laboratory confirmed cases and negative controls, matched on the basis of geography, time of sampling, specie and age. A piloted questionnaire was used to collect data regarding risk factors associated with the occurrence of EI in face to face interviews. Conditional logistic regression was performed to analyze the data. A total of 16 out of 23 variables were found associated as risk factors in Univariable conditional logistic regression analysis. Multivariable conditional logistic-regression analysis was also performed. Monthly removal of manure doubles the risk of EI (EI) compared to its daily removal. Due to lack of vaccination; the spread of disease was favored by high equine density. Investigating the index-case it was recorded that infected cases were imported from Afghanistan. Most of these risk factors related to biosecurity and management were due to low awareness level regarding EI amongst the respondents. These findings are in line with the results of many other studies identifying similar risk factors for EI infection in various countries. Adopting protective practices, vaccination and controlling the risk factors identified in the present study could reduce the spread and future outbreaks of EI in Pakistan.

Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution

BACKGROUND

Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) were analyzed to elucidate the genetic and evolutionary relationships in a novel perspective.

RESULTS

The group - specific consensus amino acid substitutions were identified in all polymerase genes of EIVs that led to divergence of EIVs into various clades. The consistent amino acid changes were also detected in the Florida clade 2 EIVs circulating in Europe and Asia since 2007. To study the codon usage patterns, a total of 281,324 codons of polymerase genes of EIV H3N8 isolates from 1963 to 2015 were systemically analyzed. The polymerase genes of EIVs exhibit a weak codon usage bias. The ENc-GC3s and Neutrality plots indicated that natural selection is the major influencing factor of codon usage bias, and that the impact of mutation pressure is comparatively minor. The methods for estimating host imposed translation pressure suggested that the polymerase acidic (PA) gene seems to be under less translational pressure compared to polymerase basic 1 (PB1) and polymerase basic 2 (PB2) genes. The multivariate statistical analysis of polymerase genes divided EIVs into four evolutionary diverged clusters - Pre-divergent, Eurasian, Florida sub-lineage 1 and 2.

CONCLUSIONS

Various lineage specific amino acid substitutions observed in all polymerase genes of EIVs and especially, clade 2 EIVs underwent major variations which led to the emergence of a phylogenetically distinct group of EIVs originating from Richmond/1/07. The codon usage bias was low in all the polymerase genes of EIVs that was influenced by the multiple factors such as the nucleotide compositions, mutation pressure, aromaticity and hydropathicity. However, natural selection was the major influencing factor in defining the codon usage patterns and evolution of polymerase genes of EIVs.

Molecular Epidemiology of a novel re-assorted epidemic strain of equine influenza virus in Pakistan in 2015-16

BACKGROUND

A widespread epidemic of equine influenza (EI) occurred in nonvaccinated equine population across multiple districts in Khyber Pakhtunkhwa Province of Pakistan during 2015-2016.

OBJECTIVES AND METHODS

An epidemiological surveillance study was conducted from Oct 2015 to April 2016 to investigate the outbreak. EI virus strains were isolated in embryonated eggs from suspected equines swab samples and were subjected to genome sequencing using M13 tagged segment specific primers. Phylogenetic analyses of the nucleotide sequences were concluded using Geneious. Haemagglutinin (HA), Neuraminidase (NA), Matrix (M) and nucleoprotein (NP) genes nucleotide and amino acid sequences of the isolated viruses were aligned with those of OIE recommended, FC-1, FC-2, and contemporary isolates of influenza A viruses from other species.

RESULTS

HA and NA genes amino acid sequences were very similar to Tennessee/14 and Malaysia/15 of FC-1 and clustered with the contemporary isolates recently reported in the USA. Phylogenetic analysis showed that these viruses were mostly identical (with 99.6% and 97.4% nucleotide homology) to, and were reassortants containing chicken/Pakistan/14 (H7N3) and Canine/Beijing/10 (H3N2) like M and NP genes. Genetic analysis indicated that A/equine/Pakistan/16 viruses were most probably the result of several re-assortments between the co-circulating avian and equine viruses, and were genetically unlike the other equine viruses due to the presence of H7N3 or H3N2 like M and NP genes.

CONCLUSION

Epidemiological data analysis indicated the potential chance of mixed, and management such as mixed farming system by keeping equine, canine and backyard poultry together in confined premises as the greater risk factors responsible for the re-assortments. Other factors might have contributed to the spread of the epidemic, including low awareness level, poor control of equine movements, and absence of border control disease strategies.

Evolution and Divergence of H3N8 Equine Influenza Viruses Circulating in the United Kingdom from 2013 to 2015

Equine influenza viruses (EIV) are a major cause of acute respiratory disease in horses worldwide and occasionally also affect vaccinated animals. Like other influenza A viruses, they undergo antigenic drift, highlighting the importance of both surveillance and virus characterisation in order for vaccine strains to be kept up to date. The aim of the work reported here was to monitor the genetic and antigenic changes occurring in EIV circulating in the UK from 2013 to 2015 and to identify any evidence of vaccine breakdown in the field. Virus isolation, reverse transcription polymerase chain reaction (RT-PCR) and sequencing were performed on EIV-positive nasopharyngeal swab samples submitted to the Diagnostic Laboratory Services at the Animal Health Trust (AHT). Phylogenetic analyses were completed for the haemagglutinin-1 (HA1) and neuraminidase (NA) genes using PhyML and amino acid sequences compared against the current World Organisation for Animal Health (OIE)-recommended Florida clade 2 vaccine strain. Substitutions between the new isolates and the vaccine strain were mapped onto the three-dimensional structure protein structures using PyMol. Antigenic analyses were carried out by haemagglutination inhibition assay using a panel of post-infection ferret antisera. Sixty-nine outbreaks of equine influenza in the UK were reported by the AHT between January 2013 and December 2015. Forty-seven viruses were successfully isolated in eggs from 41 of the outbreaks. Only three cases of vaccine breakdown were identified and in each case the vaccine used contained a virus antigen not currently recommended for equine influenza vaccines. Nucleotide sequencing of the HA and NA genes revealed that all of the viruses belonged to the Florida clade 2 sub-lineage of H3N8 EIV. Phylogenetic and sequence analyses showed that the two sub-populations, previously identified within clade 2, continued to circulate and had accrued further amino acid substitutions. Antigenic characterisation using post-infection ferret antisera in haemagglutination inhibition assays however, failed to detect any marked antigenic differences between the isolates. These findings show that Florida clade 2 EIV continue to circulate in the UK and support the current OIE recommendation to include an example of Florida clade 2 in vaccines.

Serological evidence of equine influenza virus in horse stables in Kaduna, Nigeria

Equine influenza virus (EIV) is a major cause of acute respiratory diseases in horses in most parts of the world that results in severe economic losses. Information on the epidemiology of EIV in tropical Africa is scanty. An enzyme-linked immunosorbent assay (ELISA) was used to detect the presence of influenza A virus nucleoprotein (NP) in 284 horse sera in Kaduna State, Northern Nigeria. The ELISA-positive sera were further examined for hemagglutination inhibition (HI) antibodies to two strains each of H3N8 and H7N3 subtypes of influenza A virus. The results showed that antibodies against influenza A virus nucleoprotein were detected in 60.9% (173 of 284) of horses examined by NP-ELISA. Equine H3 and H7 subtypes were detected in 60% (21 of 35) and 20% (7 of 35) of horse sera respectively across the stables. Adequate quarantine of all imported horses, a national equine influenza surveillance plan and an appropriate EIV control program in Nigeria are recommended to safeguard the large horse population.

Epidemiological and virological findings during multiple outbreaks of equine influenza in South America in 2012

Background

In 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.

Objective

To characterise the EI viruses detected during the outbreak in Uruguay and Argentina.

Methods

Virus 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.

Results

The 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.

Conclusions

The 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.

Characterisation of the epidemic strain of H3N8 equine influenza virus responsible for outbreaks in South America in 2012

Background

An extensive outbreak of equine influenza occurred across multiple countries in South America during 2012. The epidemic was first reported in Chile then spread to Brazil, Uruguay and Argentina, where both vaccinated and unvaccinated animals were affected. In Brazil, infections were widespread within 3months of the first reported cases. Affected horses included animals vaccinated with outdated vaccine antigens, but also with the OIE-recommended Florida clade 1 strain South Africa/4/03.

Methods

Equine influenza virus strains from infected horses were isolated in eggs, then a representative strain was subjected to full genome sequencing using segment-specific primers with M13 tags. Phylogenetic analyses of nucleotide sequences were completed using PhyML. Amino acid sequences of haemagglutinin and neuraminidase were compared against those of vaccine strains and recent isolates from America and Uruguay, substitutions were mapped onto 3D protein structures using PyMol. Antigenic analyses were completed by haemagglutination-inhibition assay using post-infection ferret sera.

Results

Nucleotide sequences of the haemaglutinin (HA) and neuraminidase (NA) genes of Brazilian isolate A/equine/Rio Grande do Sul/2012 were very similar to those of viruses belonging to Florida clade 1 and clustered with contemporary isolates from the USA. Comparison of their amino acid sequences against the OIE-recommended Florida clade 1 vaccine strain A/equine/South Africa/4/03 revealed five amino acid substitutions in HA and seven in NA. Changes in HA included one within antigenic site A and one within the 220-loop of the sialic acid receptor binding site. However, antigenic analysis by haemagglutination inhibition (HI) assay with ferret antisera raised against representatives of European, Kentucky and Florida sublineages failed to indicate any obvious differences in antigenicity.

Conclusions

An extensive outbreak of equine influenza in South America during 2012 was caused by a virus belonging to Florida clade 1, closely related to strains circulating in the USA in 2011. Despite reports of vaccine breakdown with products containing the recommended strain South Africa/03, no evidence was found of significant antigenic drift. Other factors may have contributed to the rapid spread of this virus, including poor control of horse movement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-016-0503-9) contains supplementary material, which is available to authorized users.

Controlling equine influenza: Traditional to next generation serological assays

Serological assays provide an indirect route for the recognition of infectious agents via the detection of antibodies against the infectious agent of interest within serum. Serological assays for equine influenza A virus can be applied for different purposes: diagnosing infections; subtyping isolates; surveillance of circulating strains; and to evaluate the efficacy of vaccines before they reach the market. Haemagglutination inhibition (HI) and single radial haemolysis (SRH) assays are most commonly used in the equine field. This review outlines how both these assays together with virus neutralization (VN) and ELISA are performed, interpreted and applied for the control of equine influenza, giving the limitations and advantages of each. The pseudotyped virus neutralization assay (PVNA) is also discussed as a promising prospect for the future of equine influenza virus serology.

Evaluation of twenty-two rapid antigen detection tests in the diagnosis of Equine Influenza caused by viruses of H3N8 subtype

Background

Equine influenza (EI) is a highly contagious disease caused by viruses of the H3N8 subtype. The rapid diagnosis of EI is essential to reduce the disease spread. Many rapid antigen detection (RAD) tests for diagnosing human influenza are available, but their ability to diagnose EI has not been systematically evaluated.

Objectives

The aim of this study was to compare the performance of 22 RAD tests in the diagnosis of EI.

Methods

The 22 RAD tests were performed on fivefold serial dilutions of EI virus to determine their detection limits. The four most sensitive RAD tests (ImmunoAce Flu, BD Flu examan, Quick chaser Flu A, B and ESPLINE Influenza A&B‐N) were further evaluated using nasopharyngeal samples collected from experimentally infected and naturally infected horses. The results were compared to those obtained using molecular tests.

Results

The detection limits of the 22 RAD tests varied hugely. Even the four RAD tests showing the best sensitivity were 125‐fold less sensitive than the molecular techniques. The duration of virus detection in the experimentally infected horses was shorter using the RAD tests than using the molecular techniques. The RAD tests detected between 27% and 73% of real‐time RT‐PCR‐positive samples from naturally infected horses.

Conclusions

The study demonstrated the importance of choosing the right RAD tests as only three of 22 were fit for diagnosing EI. It was also indicated that even RAD tests with the highest sensitivity serve only as an adjunct to molecular tests because of the potential for false‐negative results.

A Systematic Review of Recent Advances in Equine Influenza Vaccination

Equine influenza (EI) is a major respiratory disease of horses, which is still causing substantial outbreaks worldwide despite several decades of surveillance and prevention. Alongside quarantine procedures, vaccination is widely used to prevent or limit spread of the disease. The panel of EI vaccines commercially available is probably one of the most varied, including whole inactivated virus vaccines, Immuno-Stimulating Complex adjuvanted vaccines (ISCOM and ISCOM-Matrix), a live attenuated equine influenza virus (EIV) vaccine and a recombinant poxvirus-vectored vaccine. Several other strategies of vaccination are also evaluated. This systematic review reports the advances of EI vaccines during the last few years as well as some of the mechanisms behind the inefficient or sub-optimal response of horses to vaccination.

Using Bayes' rule to define the value of evidence from syndromic surveillance

In this work we propose the adoption of a statistical framework used in the evaluation of forensic evidence as a tool for evaluating and presenting circumstantial “evidence” of a disease outbreak from syndromic surveillance. The basic idea is to exploit the predicted distributions of reported cases to calculate the ratio of the likelihood of observing n cases given an ongoing outbreak over the likelihood of observing n cases given no outbreak. The likelihood ratio defines the Value of Evidence (V). Using Bayes' rule, the prior odds for an ongoing outbreak are multiplied by V to obtain the posterior odds. This approach was applied to time series on the number of horses showing clinical respiratory symptoms or neurological symptoms. The separation between prior beliefs about the probability of an outbreak and the strength of evidence from syndromic surveillance offers a transparent reasoning process suitable for supporting decision makers. The value of evidence can be translated into a verbal statement, as often done in forensics or used for the production of risk maps. Furthermore, a Bayesian approach offers seamless integration of data from syndromic surveillance with results from predictive modeling and with information from other sources such as disease introduction risk assessments.

Characteristics of respiratory tract disease in horses inoculated with equine rhinitis A virus

OBJECTIVE

To develop a method for experimental induction of equine rhinitis A virus (ERAV) infection in equids and to determine the clinical characteristics of such infection.

ANIMALS

8 ponies (age, 8 to 12 months) seronegative for antibodies against ERAV. PROCEDURES-Nebulization was used to administer ERAV (strain ERAV/ON/05; n = 4 ponies) or cell culture medium (control ponies; 4) into airways of ponies; 4 previously ERAV-inoculated ponies were reinoculated 1 year later. Physical examinations and pulmonary function testing were performed at various times for 21 days after ERAV or mock inoculation. Various types of samples were obtained for virus isolation, blood samples were obtained for serologic testing, and clinical scores were determined for various variables.

RESULTS

ERAV-inoculated ponies developed respiratory tract disease characterized by pyrexia, nasal discharge, adventitious lung sounds, and enlarged mandibular lymph nodes. Additionally, these animals had purulent mucus in lower airways up to the last evaluation time 21 days after inoculation (detected endoscopically). The virus was isolated from various samples obtained from lower and upper airways of ERAV-inoculated ponies up to 7 days after exposure; this time corresponded with an increase in serum titers of neutralizing antibodies against ERAV. None of the ponies developed clinical signs of disease after reinoculation 1 year later.

CONCLUSIONS AND CLINICAL RELEVANCE

Results of this study indicated ERAV induced respiratory tract disease in seronegative ponies. However, ponies with neutralizing antibodies against ERAV did not develop clinical signs of disease when reinoculated with the virus. Therefore, immunization of ponies against ERAV could prevent respiratory tract disease attributable to that virus in such animals.

Efficacy of a non-updated, Matrix-C-based equine influenza subunit-tetanus vaccine following Florida sublineage clade 2 challenge

Assessing the ability of current equine influenza vaccines to provide cross-protection against emerging strains is important. Horses not vaccinated previously and seronegative for equine influenza based on haemagglutination inhibition (HI) assay were assigned at random to vaccinated (n=7) or non-vaccinated (control, n=5) groups. Vaccination was performed twice four weeks apart with a 1 ml influenza subunit (A/eq/Prague/1/56, A/eq/Newmarket/1/93, A/eq/Newmarket/2/93), tetanus toxoid vaccine with Matrix-C adjuvant (EquilisPrequenza Te). All the horses were challenged individually by aerosol with A/eq/Richmond/1/07 three weeks after the second vaccination. Rectal temperature, clinical signs, serology and virus excretion were monitored for 14 days after challenge. There was no pain at the injection site or increases in rectal temperature following vaccination. Increases in rectal temperature and characteristic clinical signs were recorded in the control horses. Clinical signs were minimal in vaccinated horses. Clinical (P=0.0345) and total clinical scores (P=0.0180) were significantly lower in the vaccinated than in the control horses. Vaccination had a significant effect on indicators of viraemia – the extent (P=0.0006) and duration (P=<0.0001) of virus excretion and the total amount of virus excreted (AUC, P=0.0006). Vaccination also had a significant effect (P=0.0017) on whether a horse was positive or negative for virus excretion during the study. Further research is needed to fully understand the specific properties of this vaccine that may contribute to its cross-protective capacity.

Epidemiological and virological investigations of equine influenza outbreaks in Ireland (2010-2012)

BACKGROUND

Outbreaks of equine influenza (EI) in endemic populations cause disruption and economic loss.

OBJECTIVES

To identify (i) factors involved in the spread of EI (ii) virus strains responsible for outbreaks (iii) single radial haemolysis (SRH) antibody levels correlating with protection against current virus strains (iv) evidence of vaccination breakdown.

METHODS

RT-PCR, virus isolation and SRH were carried out on nasopharyngeal swabs and blood samples collected from horses, ponies and donkeys on affected premises. Data relating to 629 samples from 135 equidae were analysed.

RESULTS AND CONCLUSIONS

Outbreaks were sporadic, self limiting and associated with the movement of horses. Vaccination status and age influenced clinical signs of disease while housing and fomites contributed to virus spread. Subclinical infection as defined as a horse which tested positive by one or more of the following; RT-PCR, virus isolation and seroconversion in the absence of clinical signs, was identified in 9% of animals. Of the horses with up to date vaccination records 32% developed clinical signs. Vaccine breakdown occurred among horses vaccinated with all four commercially available vaccines. Analysis of HA1 sequence data generated for 26 viruses indicated that they all belonged to clade 2 of the Florida sublineage. Higher SRH antibody levels were required for both clinical and virological protection than reported in studies where vaccine strains were antigenically and genetically similar to those circulating in the field. The results of this study therefore support the OIE recommendations that vaccines be updated to include representatives of both clades of the Florida sublineage.

The genetics of virus particle shape in equine influenza A virus

Background

Many human strains of influenza A virus produce highly pleomorphic virus particles that at the extremes can be approximated as either spheres of around 100 nm diameter or filaments of similar cross‐section but elongated to lengths of many microns. The role filamentous virions play in the virus life cycle remains enigmatic.

Objectives/Methods

Here, we set out to define the morphology and genetics of virus particle shape in equine influenza A virus, using reverse genetics and microscopy of infected cells.

Results and Conclusions

The majority of H3N8 strains tested were found to produce filamentous virions, as did the prototype H7N7 A/eq/Prague/56 strain. The exception was the prototype H3N8 isolate, A/eq/Miami/63. Reassortment of equine influenza virus M genes from filamentous and non‐filamentous strains into the non‐filamentous human virus A/PR/8/34 confirmed that segment 7 is a major determinant of particle shape. Sequence analysis identified three M1 amino acid polymorphisms plausibly associated with determining virion morphology, and the introduction of these changes into viruses confirmed the importance of two: S85N and N231D. However, while either change alone affected filament production, the greatest effect was seen when the polymorphisms were introduced in conjunction. Thus, influenza A viruses from equine hosts also produce filamentous virions, and the major genetic determinants are set by the M1 protein. However, the precise sequence determinants are different to those previously identified in human or porcine viruses.