Microevolution of canine influenza virus in shelters and its molecular epidemiology in the United States

Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses

Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One example in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, FL, USA, after emerging among horses in South America. In the early 21st century, the American lineage of EIV diverged into two 'Florida' clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to reveal their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV.

Increased public health threat of avian-origin H3N2 influenza virus caused by its evolution in dogs

Influenza A viruses in animal reservoirs repeatedly cross species barriers to infect humans. Dogs are the closest companion animals to humans, but the role of dogs in the ecology of influenza viruses is unclear. H3N2 avian influenza viruses were transmitted to dogs around 2006 and have formed stable lineages. The long-term epidemic of avian-origin H3N2 virus in canines offers the best models to investigate the effect of dogs on the evolution of influenza viruses. Here, we carried out a systematic and comparative identification of the biological characteristics of H3N2 canine influenza viruses (CIVs) isolated worldwide over 10 years. We found that, during adaptation in dogs, H3N2 CIVs became able to recognize the human-like SAα2,6-Gal receptor, showed gradually increased hemagglutination (HA) acid stability and replication ability in human airway epithelial cells, and acquired a 100% transmission rate via respiratory droplets in a ferret model. We also found that human populations lack immunity to H3N2 CIVs, and even preexisting immunity derived from the present human seasonal influenza viruses cannot provide protection against H3N2 CIVs. Our results showed that canines may serve as intermediates for the adaptation of avian influenza viruses to humans. Continuous surveillance coordinated with risk assessment for CIVs is necessary.

Review of Influenza Virus Vaccines: The Qualitative Nature of Immune Responses to Infection and Vaccination Is a Critical Consideration

Influenza viruses have affected the world for over a century, causing multiple pandemics. Throughout the years, many prophylactic vaccines have been developed for influenza; however, these viruses are still a global issue and take many lives. In this paper, we review influenza viruses, associated immunological mechanisms, current influenza vaccine platforms, and influenza infection, in the context of immunocompromised populations. This review focuses on the qualitative nature of immune responses against influenza viruses, with an emphasis on trained immunity and an assessment of the characteristics of the host–pathogen that compromise the effectiveness of immunization. We also highlight innovative immunological concepts that are important considerations for the development of the next generation of vaccines against influenza viruses.

Hemagglutinin Stability and Its Impact on Influenza A Virus Infectivity, Pathogenicity, and Transmissibility in Avians, Mice, Swine, Seals, Ferrets, and Humans

Genetically diverse influenza A viruses (IAVs) circulate in wild aquatic birds. From this reservoir, IAVs sporadically cause outbreaks, epidemics, and pandemics in wild and domestic avians, wild land and sea mammals, horses, canines, felines, swine, humans, and other species. One molecular trait shown to modulate IAV host range is the stability of the hemagglutinin (HA) surface glycoprotein. The HA protein is the major antigen and during virus entry, this trimeric envelope glycoprotein binds sialic acid-containing receptors before being triggered by endosomal low pH to undergo irreversible structural changes that cause membrane fusion. The HA proteins from different IAV isolates can vary in the pH at which HA protein structural changes are triggered, the protein causes membrane fusion, or outside the cell the virion becomes inactivated. HA activation pH values generally range from pH 4.8 to 6.2. Human-adapted HA proteins tend to have relatively stable HA proteins activated at pH 5.5 or below. Here, studies are reviewed that report HA stability values and investigate the biological impact of variations in HA stability on replication, pathogenicity, and transmissibility in experimental animal models. Overall, a stabilized HA protein appears to be necessary for human pandemic potential and should be considered when assessing human pandemic risk.

Canine and Feline Influenza

Influenza virus infections of carnivores-primarily in dogs and in large and small cats-have been repeatedly observed to be caused by a number of direct spillovers of avian viruses or in infections by human or swine viruses. In addition, there have also been prolonged epizootics of an H3N8 equine influenza virus in dogs starting around 1999, of an H3N2 avian influenza virus in domestic dog populations in Asia and in the United States that started around 2004, and an outbreak of an avian H7N2 influenza virus among cats in an animal shelter in the United States in 2016. The impact of influenza viruses in domesticated companion animals and their zoonotic or panzootic potential poses significant questions for veterinary and human health.

Influenza A Virus Infection in Cats and Dogs: A Literature Review in the Light of the "One Health" Concept

Influenza A viruses are amongst the most challenging viruses that threaten both human and animal health. Constantly evolving and crossing species barrier, the emergence of novel zoonotic pathogens is one of the greatest challenges to global health security. During the last decade, considerable attention has been paid to influenza virus infections in dogs, as two canine H3N8 and H3N2 subtypes caused several outbreaks through the United States and Southern Asia, becoming endemic. Cats, even though less documented in the literature, still appear to be susceptible to many avian influenza infections. While influenza epidemics pose a threat to canine and feline health, the risks to humans are largely unknown. Here, we review most recent knowledge of the epidemiology of influenza A viruses in dogs and cats, existing evidences for the abilities of these species to host, sustain intraspecific transmission, and generate novel flu A lineages through genomic reassortment. Such enhanced understanding suggests a need to reinforce surveillance of the role played by companion animals-human interface, in light of the “One Health” concept and the potential emergence of novel zoonotic viruses.

Genetic and serologic surveillance of canine (CIV) and equine (EIV) influenza virus in Nuevo León State, México

BACKGROUND

Despite the uncontrolled distribution of the Influenza A virus through wild birds, the detection of canine influenza virus and equine influenza virus in Mexico was absent until now. Recently, outbreaks of equine and canine influenza have been reported around the world; the virus spreads quickly among animals and there is potential for zoonotic transmission.

METHODS

Amplification of the Influenza A virus matrix gene from necropsies, nasal and conjunctival swabs from trash service horses and pets/stray dogs was performed through RT-PCR. The seroprevalence was carried out through Sandwich enzyme-linked immunosorbent assay system using the M1 recombinant protein and polyclonal antibodies anti-M1.

RESULTS

The matrix gene was amplified from 13 (19.11%) nasal swabs, two (2.94%) conjunctival swabs and five (7.35%) lung necropsies, giving a total of 20 (29.41%) positive samples in a pet dog population. A total of six (75%) positive samples of equine nasal swab were amplified. Sequence analysis showed 96-99% identity with sequences of Influenza A virus matrix gene present in H1N1, H1N2 and H3N2 subtypes. The phylogenetic analysis of the sequences revealed higher identity with matrix gene sequences detected from zoonotic isolates of subtype H1N1/2009. The detection of anti-M1 antibodies in stray dogs showed a prevalence of 123 (100%) of the sampled population, whereas in horses, 114 (92.68%) positivity was obtained.

CONCLUSION

The results unveil the prevalence of Influenza A virus in the population of horses and dogs in the state of Nuevo Leon, which could indicate a possible outbreak of equine and Canine Influenza in Mexico. We suggest that the prevalence of Influenza virus in companion animals be monitored to investigate its epizootic and zoonotic potential, in addition to encouraging the regulation of vaccination in these animal species in order to improve their quality of life.

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.

Onward transmission of viruses: how do viruses emerge to cause epidemics after spillover?

The critical step in the emergence of a new epidemic or pandemic viral pathogen occurs after it infects the initial spillover host and then is successfully transmitted onwards, causing an outbreak chain of transmission within that new host population. Crossing these choke points sets a pathogen on the pathway to epidemic emergence. While many viruses spill over to infect new or alternative hosts, only a few accomplish this transition—and the reasons for the success of those pathogens are still unclear. Here, we consider this issue related to the emergence of animal viruses, where factors involved likely include the ability to efficiently infect the new animal host, the demographic features of the initial population that favour onward transmission, the level of shedding and degree of susceptibility of individuals of that population, along with pathogen evolution favouring increased replication and more efficient transmission among the new host individuals. A related form of emergence involves mutations that increased spread or virulence of an already-known virus within its usual host. In all of these cases, emergence may be due to altered viral properties, changes in the size or structure of the host populations, ease of transport, climate change or, in the case of arboviruses, to the expansion of the arthropod vectors. Here, we focus on three examples of viruses that have gained efficient onward transmission after spillover: influenza A viruses that are respiratory transmitted, HIV, a retrovirus, that is mostly blood or mucosal transmitted, and canine parvovirus that is faecal:oral transmitted. We describe our current understanding of the changes in the viruses that allowed them to overcome the barriers that prevented efficient replication and spread in their new hosts. We also briefly outline how we could gain a better understanding of the mechanisms and variability in order to better anticipate these events in the future.

This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.

H3N8 and H3N2 Canine Influenza Viruses: Understanding These New Viruses in Dogs

Two different influenza A viruses have infected and spread among dogs since 2000, and both have been widespread in dogs in North America. The H3N8 canine influenza virus arose in the United States as a variant of equine influenza virus. The H3N2 canine influenza virus arose in Asia by transfer of an avian influenza virus to dogs. Both viruses cause mild respiratory disease and are associated with outbreaks in densely housed dogs or those with frequent connections to other dogs. The 2 canine influenza viruses each caused widespread epidemics over at least several years that were associated with localized outbreaks.

A Comprehensive Review on Equine Influenza Virus: Etiology, Epidemiology, Pathobiology, Advances in Developing Diagnostics, Vaccines, and Control Strategies

Among all the emerging and re-emerging animal diseases, influenza group is the prototype member associated with severe respiratory infections in wide host species. Wherein, Equine influenza (EI) is the main cause of respiratory illness in equines across globe and is caused by equine influenza A virus (EIV-A) which has impacted the equine industry internationally due to high morbidity and marginal morality. The virus transmits easily by direct contact and inhalation making its spread global and leaving only limited areas untouched. Hitherto reports confirm that this virus crosses the species barriers and found to affect canines and few other animal species (cat and camel). EIV is continuously evolving with changes at the amino acid level wreaking the control program a tedious task. Until now, no natural EI origin infections have been reported explicitly in humans. Recent advances in the diagnostics have led to efficient surveillance and rapid detection of EIV infections at the onset of outbreaks. Incessant surveillance programs will aid in opting a better control strategy for this virus by updating the circulating vaccine strains. Recurrent vaccination failures against this virus due to antigenic drift and shift have been disappointing, however better understanding of the virus pathogenesis would make it easier to design effective vaccines predominantly targeting the conserved epitopes (HA glycoprotein). Additionally, the cold adapted and canarypox vectored vaccines are proving effective in ceasing the severity of disease. Furthermore, better understanding of its genetics and molecular biology will help in estimating the rate of evolution and occurrence of pandemics in future. Here, we highlight the advances occurred in understanding the etiology, epidemiology and pathobiology of EIV and a special focus is on designing and developing effective diagnostics, vaccines and control strategies for mitigating the emerging menace by EIV.

Emergence and Evolution of Novel Reassortant Influenza A Viruses in Canines in Southern China

The capacity of influenza A viruses (IAVs) to host jump from animal reservoir species to humans presents an ongoing pandemic threat. Birds and swine are considered major reservoirs of viral genetic diversity, whereas equines and canines have historically been restricted to one or two stable IAV lineages with no transmission to humans. Here, by sequencing the complete genomes of 16 IAVs obtained from canines in southern China (Guangxi Zhuang Autonomous Region [Guangxi]) in 2013 to 2015, we demonstrate that the evolution of canine influenza viruses (CIVs) in Asian dogs is increasingly complex, presenting a potential threat to humans. First, two reassortant H1N1 virus genotypes were introduced independently from swine into canines in Guangxi, including one genotype associated with a zoonotic infection. The genomes contain segments from three lineages that circulate in swine in China: North American triple reassortant H3N2, Eurasian avian-like H1N1, and pandemic H1N1. Furthermore, the swine-origin H1N1 viruses have transmitted onward in canines and reassorted with the CIV-H3N2 viruses that circulate endemically in Asian dogs, producing three novel reassortant CIV genotypes (H1N1r, H1N2r, and H3N2r [r stands for reassortant]). CIVs from this study were collected primarily from pet dogs presenting with respiratory symptoms at veterinary clinics, but dogs in Guangxi are also raised for meat, and street dogs roam freely, creating a more complex ecosystem for CIV transmission. Further surveillance is greatly needed to understand the full genetic diversity of CIV in southern China, the nature of viral emergence and persistence in the region’s diverse canine populations, and the zoonotic risk as the viruses continue to evolve.

Mammals have emerged as critically underrecognized sources of influenza virus diversity, including pigs that were the source of the 2009 pandemic and bats and bovines that harbor highly divergent viral lineages. Here, we identify two reassortant IAVs that recently host switched from swine to canines in southern China, including one virus with known zoonotic potential. Three additional genotypes were generated via reassortment events in canine hosts, demonstrating the capacity of dogs to serve as “mixing vessels.” The continued expansion of IAV diversity in canines with high human contact rates requires enhanced surveillance and ongoing evaluation of emerging pandemic threats.

Seroprevalence of three influenza A viruses (H1N1, H3N2, and H3N8) in pet dogs presented to a veterinary hospital in Ohio

The prevalence of canine H3N8 influenza and human H1N1 and H3N2 influenza in dogs in Ohio was estimated by conducting serologic tests on 1,082 canine serum samples. In addition, risk factors, such as health status and age were examined. The prevalences of human H1N1, H3N2, and canine H3N8 influenzas were 4.0%, 2.4%, and 2.3%, respectively. Two samples were seropositive for two subtypes (H1N1 and H3N2; H1N1 and canine influenza virus [CIV] H3N8). Compared to healthy dogs, dogs with respiratory signs were 5.795 times more likely to be seropositive against H1N1 virus (p = 0.042). The prevalence of human flu infection increased with dog age and varied by serum collection month. The commercial enzyme-linked immunosorbent assay used in this study did not detect nucleoprotein-specific antibodies from many hemagglutination inhibition positive sera, which indicates a need for the development and validation of rapid tests for influenza screening in canine populations. In summary, we observed low exposure of dogs to CIV and human influenza viruses in Ohio but identified potential risk factors for consideration in future investigations. Our findings support the need for establishment of reliable diagnostic standards for serologic detection of influenza infection in canine species.

A bivalent live-attenuated influenza vaccine for the control and prevention of H3N8 and H3N2 canine influenza viruses

Canine influenza viruses (CIVs) cause a contagious respiratory disease in dogs. CIV subtypes include H3N8, which originated from the transfer of H3N8 equine influenza virus (EIV) to dogs; and the H3N2, which is an avian-origin virus adapted to infect dogs. Only inactivated influenza vaccines (IIVs) are currently available against the different CIV subtypes. However, the efficacy of these CIV IIVs is not optimal and improved vaccines are necessary for the efficient prevention of disease caused by CIVs in dogs. Since live-attenuated influenza vaccines (LAIVs) induce better immunogenicity and protection efficacy than IIVs, we have combined our previously described H3N8 and H3N2 CIV LAIVs to create a bivalent vaccine against both CIV subtypes. Our findings show that, in a mouse model of infection, the bivalent CIV LAIV is safe and able to induce, upon a single intranasal immunization, better protection than that induced by a bivalent CIV IIV against subsequent challenge with H3N8 or H3N2 CIVs. These protection results also correlated with the ability of the bivalent CIV LAIV to induce better humoral immune responses. This is the first description of a bivalent LAIV for the control and prevention of H3N8 and H3N2 CIV infections in dogs.

A live-attenuated influenza vaccine for H3N2 canine influenza virus

Canine influenza is a contagious respiratory disease in dogs caused by two subtypes (H3N2 and H3N8) of canine influenza virus (CIV). Currently, only inactivated influenza vaccines (IIVs) are available for the prevention of CIVs. Historically, live-attenuated influenza vaccines (LAIVs) have been shown to produce better immunogenicity and protection efficacy than IIVs. Here, we have engineered a CIV H3N2 LAIV by using the internal genes of a previously described CIV H3N8 LAIV as a master donor virus (MDV) and the surface HA and NA genes of a circulating CIV H3N2 strain. Our findings show that CIV H3N2 LAIV replicates efficiently at low temperature but its replication is impaired at higher temperatures. The CIV H3N2 LAIV was attenuated in vivo but induced better protection efficacy in mice against challenge with wild-type CIV H3N2 than a commercial CIV H3N2 IIV. This is the first description of a LAIV for the prevention of CIV H3N2 in dogs.

Temperature-Sensitive Live-Attenuated Canine Influenza Virus H3N8 Vaccine

Canine influenza is a respiratory disease of dogs caused by canine influenza virus (CIV). CIV subtypes responsible for influenza in dogs include H3N8, which originated from the transfer of H3N8 equine influenza virus to dogs; and the H3N2 CIV, which is an avian-origin virus that adapted to infect dogs. Influenza infections are most effectively prevented through vaccination to reduce transmission and future infection. Currently, only inactivated influenza vaccines (IIVs) are available for the prevention of CIV in dogs. However, the efficacy of IIVs is suboptimal, and novel approaches are necessary for the prevention of disease caused by this canine respiratory pathogen. Using reverse genetics techniques, we have developed a live-attenuated CIV vaccine (LACIV) for the prevention of H3N8 CIV. The H3N8 LACIV replicates efficiently in canine cells at 33°C but is impaired at temperatures of 37 to 39°C and was attenuated compared to wild-type H3N8 CIV in vivo and ex vivo The LACIV was able to induce protection against H3N8 CIV challenge with a single intranasal inoculation in mice. Immunogenicity and protection efficacy were better than that observed with a commercial CIV H3N8 IIV but provided limited cross-reactive immunity and heterologous protection against H3N2 CIV. These results demonstrate the feasibility of implementing a LAIV approach for the prevention and control of H3N8 CIV in dogs and suggest the need for a new LAIV for the control of H3N2 CIV.

IMPORTANCE

Two influenza A virus subtypes has been reported in dogs in the last 16 years: the canine influenza viruses (CIV) H3N8 and H3N2 of equine and avian origins, respectively. To date, only inactivated influenza vaccines (IIVs) are available to prevent CIV infections. Here, we report the generation of a recombinant, temperature-sensitive H3N8 CIV as a live-attenuated influenza vaccine (LAIV), which was attenuated in mice and dog tracheal, explants compared to CIV H3N8 wild type. A single dose of H3N8 LACIV showed immunogenicity and protection against a homologous challenge that was better than that conferred with an H3N8 IIV, demonstrating the feasibility of implementing a LAIV approach for the improved control of H3N8 CIV infections in dogs.

The ecology and adaptive evolution of influenza A interspecies transmission

Since 2013, there have been several alarming influenza-related events; the spread of highly pathogenic avian influenza H5 viruses into North America, the detection of H10N8 and H5N6 zoonotic infections, the ongoing H7N9 infections in China and the continued zoonosis of H5N1 viruses in parts of Asia and the Middle East. The risk of a new influenza pandemic increases with the repeated interspecies transmission events that facilitate reassortment between animal influenza strains; thus, it is of utmost importance to understand the factors involved that promote or become a barrier to cross-species transmission of Influenza A viruses (IAVs). Here, we provide an overview of the ecology and evolutionary adaptations of IAVs, with a focus on a review of the molecular factors that enable interspecies transmission of the various virus gene segments.

Canine influenza viruses with modified NS1 proteins for the development of live-attenuated vaccines

Canine Influenza Virus (CIV) H3N8 is the causative agent of canine influenza, a common and contagious respiratory disease of dogs. Currently, only inactivated influenza vaccines (IIVs) are available for the prevention of CIV H3N8. However, live-attenuated influenza vaccines (LAIVs) are known to provide better immunogenicity and protection efficacy than IIVs. Influenza NS1 is a virulence factor that offers an attractive target for the preparation of attenuated viruses as LAIVs. Here we generated recombinant H3N8 CIVs containing truncated or a deleted NS1 protein to test their potential as LAIVs. All recombinant viruses were attenuated in mice and showed reduced replication in cultured canine tracheal explants, but were able to confer complete protection against challenge with wild-type CIV H3N8 after a single intranasal immunization. Immunogenicity and protection efficacy was better than that observed with an IIV. This is the first description of a LAIV for the prevention of H3N8 CIV in dogs.

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.

Influenza virus vaccine for neglected hosts: horses and dogs

This study provides information regarding vaccine research and the epidemiology of influenza virus in neglected hosts (horses and dogs). Equine influenza virus (EIV) causes a highly contagious disease in horses and other equids, and outbreaks have occurred worldwide. EIV has resulted in costly damage to the horse industry and has the ability of cross the host species barrier from horses to dogs. Canine influenza is a virus of equine or avian origin and infects companion animals that live in close contact with humans; this results in possible exposure to the seasonal epizootic influenza virus. There have been case reports of genetic reassortment between human and canine influenza viruses, which results in high virulence and the ability of transmission to ferrets. This emphasizes the need for vaccine research on neglected hosts to update knowledge on current strains and to advance technology for controlling influenza outbreaks for public health.

The avian-origin H3N2 canine influenza virus that recently emerged in the United States has limited replication in swine

Equine‐origin H3N8 has circulated in dogs in the United States since 1999. A genetically and antigenically distinct avian‐origin H3N2 canine influenza was detected in March of 2015 in Chicago, Illinois. Subsequent outbreaks were reported with over 1000 dogs in the Midwest affected followed by 23 additional states with detections within 5 months. The potential for canine‐to‐swine transmission was unknown. Experimental infection in pigs showed this virus does not replicate efficiently in swine.

Equine influenza A(H3N8) virus isolated from Bactrian camel, Mongolia

Because little is known about the ecology of influenza viruses in camels, 460 nasal swab specimens were collected from healthy (no overt illness) Bactrian camels in Mongolia during 2012. One specimen was positive for influenza A virus (A/camel/Mongolia/335/2012[H3N8]), which is phylogenetically related to equine influenza A(H3N8) viruses and probably represents natural horse-to-camel transmission.

Equine and Canine Influenza H3N8 Viruses Show Minimal Biological Differences Despite Phylogenetic Divergence

The A/H3N8 canine influenza virus (CIV) emerged from A/H3N8 equine influenza virus (EIV) around the year 2000 through the transfer of a single virus from horses to dogs. We defined and compared the biological properties of EIV and CIV by examining their genetic variation, infection, and growth in different cell cultures, receptor specificity, hemagglutinin (HA) cleavage, and infection and growth in horse and dog tracheal explant cultures. Comparison of sequences of viruses from horses and dogs revealed mutations that may be linked to host adaptation and tropism. We prepared infectious clones of representative EIV and CIV strains that were similar to the consensus sequences of viruses from each host. The rescued viruses, including HA and neuraminidase (NA) double reassortants, exhibited similar degrees of long-term growth in MDCK cells. Different host cells showed various levels of susceptibility to infection, but no differences in infectivity were seen when comparing viruses. All viruses preferred α2-3- over α2-6-linked sialic acids for infections, and glycan microarray analysis showed that EIV and CIV HA-Fc fusion proteins bound only to α2-3-linked sialic acids. Cleavage assays showed that EIV and CIV HA proteins required trypsin for efficient cleavage, and no differences in cleavage efficiency were seen. Inoculation of the viruses into tracheal explants revealed similar levels of infection and replication by each virus in dog trachea, although EIV was more infectious in horse trachea than CIV.

IMPORTANCE

Influenza A viruses can cross species barriers and cause severe disease in their new hosts. Infections with highly pathogenic avian H5N1 virus and, more recently, avian H7N9 virus have resulted in high rates of lethality in humans. Unfortunately, our current understanding of how influenza viruses jump species barriers is limited. Our aim was to provide an overview and biological characterization of H3N8 equine and canine influenza viruses using various experimental approaches, since the canine virus emerged from horses approximately 15 years ago. We showed that although there were numerous genetic differences between the equine and canine viruses, this variation did not result in dramatic biological differences between the viruses from the two hosts, and the viruses appeared phenotypically equivalent in most assays we conducted. These findings suggest that the cross-species transmission and adaptation of influenza viruses may be mediated by subtle changes in virus biology.

Origins and Evolutionary Dynamics of H3N2 Canine Influenza Virus

Influenza A viruses (IAVs) are maintained mainly in wild birds, and despite frequent spillover infections of avian IAVs into mammals, only a small number of viruses have become established in mammalian hosts. A new H3N2 canine influenza virus (CIV) of avian origin emerged in Asia in the mid-2000s and is now circulating in dog populations of China and South Korea, and possibly in Thailand. The emergence of CIV provides new opportunities for zoonotic infections and interspecies transmission. We examined 14,764 complete IAV genomes together with all CIV genomes publicly available since its first isolation until 2013. We show that CIV may have originated as early as 1999 as a result of segment reassortment among Eurasian and North American avian IAV lineages. We also identified amino acid changes that might have played a role in CIV emergence, some of which have not been previously identified in other cross-species jumps. CIV evolves at a lower rate than H3N2 human influenza viruses do, and viral phylogenies exhibit geographical structure compatible with high levels of local transmission. We detected multiple intrasubtypic and heterosubtypic reassortment events, including the acquisition of the NS segment of an H5N1 avian influenza virus that had previously been overlooked. In sum, our results provide insight into the adaptive changes required by avian viruses to establish themselves in mammals and also highlight the potential role of dogs to act as intermediate hosts in which viruses with zoonotic and/or pandemic potential could originate, particularly with an estimated dog population of ∼ 700 million.

IMPORTANCE

Influenza A viruses circulate in humans and animals. This multihost ecology has important implications, as past pandemics were caused by IAVs carrying gene segments of both human and animal origin. Adaptive evolution is central to cross-species jumps, and this is why understanding the evolutionary processes that shape influenza A virus genomes is key to elucidating the mechanisms underpinning viral emergence. An avian-origin canine influenza virus (CIV) has recently emerged in dogs and is spreading in Asia. We reconstructed the evolutionary history of CIV and show that it originated from both Eurasian and North American avian lineages. We also identified the mutations that might have been responsible for the cross-species jump. Finally, we provide evidence of multiple reassortment events between CIV and other influenza viruses (including an H5N1 avian virus). This is a cause for concern, as there is a large global dog population to which humans are highly exposed.

Influenza virus reservoirs and intermediate hosts: dogs, horses, and new possibilities for influenza virus exposure of humans

Influenza A virus (IAV) infections in hosts outside the main aquatic bird reservoirs occur periodically. Although most such cross-species transmission events result in limited onward transmission in the new host, sustained influenza outbreaks have occurred in poultry and in a number of mammalian species, including humans, pigs, horses, seals, and mink. Recently, two distinct strains of IAV have emerged in domestic dogs, with each circulating widely for several years. Here, we briefly outline what is known about the role of intermediate hosts in influenza emergence, summarize our knowledge of the new canine influenza viruses (CIVs) and how they provide key new information on the process of host adaptation, and assess the risk these viruses pose to human populations.

Contact heterogeneity, rather than transmission efficiency, limits the emergence and spread of canine influenza virus

Host-range shifts in influenza virus are a major risk factor for pandemics. A key question in the study of emerging zoonoses is how the evolution of transmission efficiency interacts with heterogeneity in contact patterns in the new host species, as this interplay influences disease dynamics and prospects for control. Here we use a synergistic mixture of models and data to tease apart the evolutionary and demographic processes controlling a host-range shift in equine H3N8-derived canine influenza virus (CIV). CIV has experienced 15 years of continuous transfer among dogs in the United States, but maintains a patchy distribution, characterized by sporadic short-lived outbreaks coupled with endemic hotspots in large animal shelters. We show that CIV has a high reproductive potential in these facilities (mean R₀ = 3.9) and that these hotspots act as refugia from the sparsely connected majority of the dog population. Intriguingly, CIV has evolved a transmission efficiency that closely matches the minimum required to persist in these refugia, leaving it poised on the extinction/invasion threshold of the host contact network. Corresponding phylogenetic analyses show strong geographic clustering in three US regions, and that the effective reproductive number of the virus (R_e) in the general dog population is close to 1.0. Our results highlight the critical role of host contact structure in CIV dynamics, and show how host contact networks could shape the evolution of pathogen transmission efficiency. Importantly, efficient control measures could eradicate the virus, in turn minimizing the risk of future sustained transmission among companion dogs that could represent a potential new axis to the human-animal interface for influenza.

Influenza virus infects a range of vertebrate hosts, including domesticated animals as well as humans. Some of the most serious influenza pandemics in humans have involved host range shifts, when an influenza virus jumps from one host species to another. Importantly, however, host range shifts do not always cause pandemics. Rather, epidemiological patterns tend to be unpredictable in new host species, causing disease patterns that change over space and time. In this paper, we analyze epidemiological and evolutionary dynamics of canine influenza virus (CIV), which jumped to dogs in the late 1990s from an equine strain (EIV) prevalent in horses. We show that the epidemiology and evolution of CIV is strongly influenced by heterogeneous patterns of infectious contact among dogs in the US. A few large populations in metropolitan animal shelters serve as reservoirs for CIV, but the virus cannot be maintained for long in smaller facilities or in the companion dog population without input from the larger shelters, which represent disease hotspots. These hotspot dynamics give a clear picture of what can happen in the time between the beginning of a host range shift and the onset of a possible pandemic, allowing more targeted strategies for control and eradication.

Evolution of the hemagglutinin gene of H3N8 canine influenza virus in dogs

With the widespread use of a recently developed canine influenza virus (CIV) H3N8 vaccine, continual molecular evaluation of circulating CIVs is necessary for monitoring antigenic drift. The aim of this project was to further describe the genetic evolution of CIV, as well as determine any genetic variation within potential antigenic regions that might result in antigenic drift. To this end, the hemagglutinin gene of 19 CIV isolates from dogs residing in Colorado, New York, and South Carolina humane shelters was sequenced and compared to CIV strains isolated during 2003–2012. Phylogenetic analysis suggests that CIV might be diverging into two geographically distinct lineages. Using a mixed-effects model for evolution and single likelihood ancestor counting methods, several amino acid sites were found to be undergoing selection pressure. Additionally, a total of six amino acid changes were observed in two possible antigenic sites for CIVs isolated from Colorado and New York humane shelters between 2009 and 2011. As CIV isolates might be diverging into geographically distinct lineages, further experiments are warranted to determine the extent of antigenic drift occurring within circulating CIV.

Detection of respiratory viruses and Bordetella bronchiseptica in dogs with acute respiratory tract infections

Canine infectious respiratory disease (CIRD) is an acute, highly contagious disease complex caused by a variety of infectious agents. At present, the role of viral and bacterial components as primary or secondary pathogens in CIRD is not fully understood. The aim of this study was to investigate the prevalence of canine parainfluenza virus (CPIV), canine adenovirus type 2 (CAV-2), canine influenza virus (CIV), canine respiratory coronavirus (CRCoV), canine herpes virus-1 (CHV-1), canine distemper virus (CDV) and Bordetella bronchiseptica in dogs with CIRD and to compare the data with findings in healthy dogs. Sixty-one dogs with CIRD and 90 clinically healthy dogs from Southern Germany were prospectively enrolled in this study. Nasal and pharyngeal swabs were collected from all dogs and were analysed for CPIV, CAV-2, CIV, CRCoV, CHV-1, CDV, and B. bronchiseptica by real-time PCR.

In dogs with acute respiratory signs, 37.7% tested positive for CPIV, 9.8% for CRCoV and 78.7% for B. bronchiseptica. Co-infections with more than one agent were detected in 47.9% of B. bronchiseptica-positive, 82.6% of CPIV-positive, and 100% of CRCoV-positive dogs. In clinically healthy dogs, 1.1% tested positive for CAV-2, 7.8% for CPIV and 45.6% for B. bronchiseptica. CPIV and B. bronchiseptica were detected significantly more often in dogs with CIRD than in clinically healthy dogs (P < 0.001 for each pathogen) and were the most common infectious agents in dogs with CIRD in Southern Germany. Mixed infections with several pathogens were common. In conclusion, clinically healthy dogs can carry respiratory pathogens and could act as sources of infection for susceptible dogs.

Epidemiology and ecology of H3N8 canine influenza viruses in US shelter dogs

BACKGROUND

H3N8 canine influenza virus (CIV) infection might contribute to increased duration of shelter stay for dogs. Greater understanding of factors contributing to CIV within shelters could help veterinarians identify control measures for CIV.

OBJECTIVES

To assess community to shelter dog CIV transmission, estimate true prevalence of CIV, and determine risk factors associated with CIV in humane shelters.

ANIMALS

5,160 dogs upon intake or discharge from 6 US humane shelters, December 2009 through January 2012.

METHODS

A cross-sectional study was performed with prospective convenience sampling of 40 dogs from each shelter monthly. Nasal swabs and serum samples were collected. Hemagglutination inhibition and real-time reverse transcriptase-polymerase chain reaction assays were performed for each nasal and serum sample. True prevalence was estimated by stochastic latent class analysis. Logistic regression was used to identify risk factors associated with CIV shedding and seropositivity.

RESULTS

Nasal swabs were positive from 4.4% of New York (NY), 4.7% of Colorado (CO), 3.2% of South Carolina, 1.2% of Florida, and 0% of California and Texas shelter dogs sampled. Seropositivity was the highest in the CO shelter dogs at 10%, and NY at 8.5%. Other shelters had 0% seropositivity. Information-theoretic analyses suggested that CIV shedding was associated with region, month, and year (model weight = 0.95) and comingling/cohousing (model weight = 0.92).

CONCLUSIONS AND CLINICAL IMPORTANCE

Community dogs are a likely source of CIV introduction into humane shelters and once CIV has become established, dog-to-dog transmission maintains the virus within a shelter.

Emerging animal viruses: real threats or simple bystanders?

The list of animal viruses has been frequently added of new members raising permanent concerns to virologists and veterinarians. The pathogenic potential and association with disease have been clearly demonstrated for some, but not for all of these emerging viruses. This review describes recent discoveries of animal viruses and their potential relevance for veterinary practice. Dogs were considered refractory to influenza viruses until 2004, when an influenza A virus subtype H3N8 was transmitted from horses and produced severe respiratory disease in racing greyhounds in Florida/USA. The novel virus, named canine influenza virus (CIV), is considered now a separate virus lineage and has spread among urban canine population in the USA. A new pestivirus (Flaviviridae), tentatively called HoBi-like pestivirus, was identified in 2004 in commercial fetal bovine serum from Brazil. Hobi-like viruses are genetically and antigenically related to bovine viral diarrhea virus (BVDV) and induce similar clinical manifestations. These novel viruses seem to be widespread in Brazilian herds and have also been detected in Southeast Asia and Europe. In 2011, a novel mosquito-borne orthobunyavirus, named Schmallenberg virus (SBV), was associated with fever, drop in milk production, abortion and newborn malformation in cattle and sheep in Germany. Subsequently, the virus disseminated over several European countries and currently represents a real treat for animal health. The origin of SBV is still a matter of debate but it may be a reassortant from previous known bunyaviruses Shamonda and Satuperi. Hepatitis E virus (HEV, family Hepeviridae) is a long known agent of human acute hepatitis and in 1997 was first identified in pigs. Current data indicates that swine HEV is spread worldwide, mainly associated with subclinical infection. Two of the four HEV genotypes are zoonotic and may be transmitted between swine and human by contaminated water and undercooked pork meat. The current distribution and impact of HEV infection in swine production are largely unknown. Avian gyrovirus type 2 (AGV2) is a newly described Gyrovirus, family Circoviridae, which was unexpectedly found in sera of poultry suspected to be infected with chicken anemia virus (CAV). AGV2 is closely related to CAV but displays sufficient genomic differences to be classified as a distinct species. AGV2 seems to be distributed in Brazil and also in other countries but its pathogenic role for chickens is still under investigation. Finally, the long time and intensive search for animal relatives of human hepatitis C virus (HCV) has led to the identification of novel hepaciviruses in dogs (canine hepacivirus [CHV]), horses (non-primate hepaciviruses [NPHV] or Theiler's disease associated virus [TDAV]) and rodents. For these, a clear and definitive association with disease is still lacking and only time and investigation will tell whether they are real disease agents or simple spectators.

Viral substitution rate variation can arise from the interplay between within-host and epidemiological dynamics

The evolutionary rates of RNA viruses can differ from one another by several orders of magnitude. Much of this variation has been explained by differences in viral mutation rates and selective environments. However, substitution rates also vary considerably across viral populations belonging to the same species. In particular, viral lineages from epidemic regions tend to have higher substitution rates than those from endemic regions, and lineages from populations with higher contact rates tend to have higher substitution rates than those from populations with lower contact rates. We address the mechanism behind these patterns by using a nested modeling approach, whereby we integrate within-host viral replication dynamics with a population-level epidemiological model. Through numerical simulations and analytical approximations, we show that variation in viral substitution rates over the course of an infection, coupled with differences in age of infection of transmitting hosts under different epidemiological scenarios, can explain these evolutionary patterns. We further derive analytical estimates of expected substitution rate differences under epidemic versus endemic epidemiological conditions. By comparing these estimates to empirical data for four viral species, we show that these factors are sufficient to explain observed variation in substitution rates in three of four cases. This work shows that even in neutrally evolving viral populations, epidemiological dynamics can alter substitution rates via the interplay between within-host replication dynamics and population-level disease dynamics.

Phylodynamic analysis of the emergence and epidemiological impact of transmissible defective dengue viruses

Intra-host sequence data from RNA viruses have revealed the ubiquity of defective viruses in natural viral populations, sometimes at surprisingly high frequency. Although defective viruses have long been known to laboratory virologists, their relevance in clinical and epidemiological settings has not been established. The discovery of long-term transmission of a defective lineage of dengue virus type 1 (DENV-1) in Myanmar, first seen in 2001, raised important questions about the emergence of transmissible defective viruses and their role in viral epidemiology. By combining phylogenetic analyses and dynamical modeling, we investigate how evolutionary and ecological processes at the intra-host and inter-host scales shaped the emergence and spread of the defective DENV-1 lineage. We show that this lineage of defective viruses emerged between June 1998 and February 2001, and that the defective virus was transmitted primarily through co-transmission with the functional virus to uninfected individuals. We provide evidence that, surprisingly, this co-transmission route has a higher transmission potential than transmission of functional dengue viruses alone. Consequently, we predict that the defective lineage should increase overall incidence of dengue infection, which could account for the historically high dengue incidence reported in Myanmar in 2001–2002. Our results show the unappreciated potential for defective viruses to impact the epidemiology of human pathogens, possibly by modifying the virulence-transmissibility trade-off, or to emerge as circulating infections in their own right. They also demonstrate that interactions between viral variants, such as complementation, can open new pathways to viral emergence.

Defective viruses are viral particles with genetic mutations or deletions that eliminate essential functions, so that they cannot complete their life cycles independently. They can reproduce only by co-infecting host cells with functional viruses and ‘borrowing’ their functional elements. Defective viruses have been observed for many human pathogens, but they have not been thought to impact epidemiological outcomes. Recently it was reported that a lineage of defective dengue virus spread through humans and mosquitoes in Myanmar for at least 18 months in 2001–2002. In this study, we investigate the emergence and epidemiological impact of this defective lineage by combining genetic sequence analyses with mathematical models. We show that the defective lineage emerged from circulating dengue viruses between June 1998 and February 2001, and that it spreads because—surprisingly—its presence causes functional dengue viruses to transmit more efficiently. Our model shows that this would cause a substantial rise in total dengue infections, consistent with historically high levels of dengue cases reported in Myanmar during 2001 and 2002. Our study yields new insights into the biology of dengue virus, and demonstrates a previously unappreciated potential for defective viruses to impact the epidemiology of infectious diseases.

Acquisition of a novel eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site confers intracellular cleavage of an H7N7 influenza virus hemagglutinin

A critical feature of highly pathogenic avian influenza viruses (H5N1 and H7N7) is the efficient intracellular cleavage of the hemagglutinin (HA) protein. H7N7 viruses also exist in equine species, and a unique feature of the equine H7N7 HA is the presence of an eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site. Here, we show that three histidine residues within the unique insertion of the equine H7N7 HA are essential for intracellular cleavage. An asparagine residue within the insertion-derived glycosylation site was also found to be essential for intracellular cleavage. The presence of the histidine residues also appear to be involved in triggering fusion, since mutation of the histidine residues resulted in a destabilizing effect. Importantly, the addition of a tetrabasic site and the eleven amino acid insertion conferred efficient intracellular cleavage to the HA of an H7N3 low pathogenicity avian influenza virus. Our studies show that acquisition of the eleven amino acid insertion offers an alternative mechanism for intracellular cleavage of influenza HA.

Diagnostic performance of the canine Influenza A Virus subtype H3N8 hemagglutination inhibition assay

Canine Influenza A virus subtype H3N8 (H3N8 CIV) was recognized in 2004 as a novel respiratory pathogen for dogs. To date, infections have been diagnosed in thousands of dogs in 38 U.S. states. Diagnostic techniques such as reverse transcription polymerase chain reaction (RT-PCR) and virus isolation may yield false-negative results if samples are collected after virus shedding has ceased. Therefore, serology is often necessary to confirm diagnosis. The hemagglutination inhibition (HI) assay is the test of choice for serological diagnosis of influenza infections in animals. However, discrepancies exist between diagnostic laboratories and research groups in some of the test parameters for the H3N8 CIV HI assay and the cutoff antibody titer for seropositivity. The objectives of the current study were 1) to assess the diagnostic performance of a H3N8 CIV HI assay using field sera from canine infectious respiratory disease outbreaks and 2) to evaluate the effect of test parameter variations on test performance, including the use of different red blood cell (RBC) species, serum treatment methods, and virus isolates. Based on a receiver operating characteristic analysis using serum microneutralization assay titers as the gold standard, the H3N8 CIV HI assay described in the present study is highly sensitive (99.6%) and specific (94.6%) when the cutoff antibody titer for seropositivity is 32. Evaluation of parameter variations determined that the sensitivity and specificity of the H3N8 CIV HI assay depend on serum pretreatment with a receptor-destroying enzyme or periodate, use of 0.5% turkey or chicken RBCs, and use of antigenically well-matched H3N8 virus strains.

Generation of reassortant influenza viruses within the non-industrial poultry system

We compared the genetic and biologic characteristics of 35 influenza viruses of different epidemiological backgrounds in Korea, including H3N2 canine influenza virus (CIV). Phylogenetic analysis revealed that chicken adapted H9N2 viruses (A/chicken/Korea/96006/96 [CK/Kor/96006-like]) have acquired aquatic avian gene segments through reassortment, and these reassorted H9N2 viruses were more frequently detected from minor poultry species than from industrial poultry. Conversely, gene segments from CK/Kor/96006-like viruses were also detected in most of the viruses from domestic ducks. Interestingly, domestic ducks, rather than wild aquatic birds, harbored close relatives of all eight gene segments of H3N2 CIV, which preferred binding to avian receptors. Therefore, bidirectional virus transmission events are assumed to have occurred between land-based poultry and aquatic poultry, in particular within the non-industrial poultry system. These events have contributed to the generation of a novel reassortant, H3N2 CIV. To prevent generating other reassortants capable of interspecies transmission, gene movements in the non-industrial poultry systems should be clarified and managed.

Serological evidence of H3N8 canine influenza-like virus circulation in USA dogs prior to 2004

H3N8 canine influenza virus (H3N8 CIV) was first reported as a novel canine respiratory pathogen in racing greyhounds and shelter dogs in the U.S.A. in 2004. Phylogenetic analyses determined that this host-adapted pathogen originated from interspecies transmission of an equine influenza virus (EIV), but it is unknown when the transmission occurred prior to discovery in 2004. The objective of this study was to determine if racing greyhound and shelter dog sera collected from 1984 to 2004 had serological evidence of exposure to H3N8 CIV or EIV. Archived sera from 702 racing greyhounds and 1568 shelter dogs were tested for H3 antibodies to the original 2004 CIV isolate, as well as EIV isolates from 1991 to 1999. None of the racing greyhounds from 1984 and 1985 had detectable H3 antibodies. One of the shelter dogs, which entered a north Florida shelter in 2004, was seropositive. For racing greyhounds sampled from 1999 to 2004, 133/520 (26%) dogs had antibodies to both CIV and EIV H3 proteins. The annual seroprevalence was 27% in 1999, 28% in 2000, 10% in 2001, 1% in 2002, 41% in 2003, and 28% in 2004. The odds of H3 seropositivity were greater among dogs that raced > or =6 months, raced on > or =2 tracks, and raced in 1998, 2002, and 2003. Many of the seropositive dogs raced at tracks that were involved in 'kennel cough' epidemics in 1998-1999 and 2002-2003. Based on serological evidence, a H3N8 canine influenza-like virus was circulating in racing greyhounds in the U.S.A. as early as 1999.

Interspecies transmission of the canine influenza H3N2 virus to domestic cats in South Korea, 2010

In the past 4 years, incidences of endemic or epidemic respiratory diseases associated with canine influenza H3N2 virus in Asian dogs have been reported in countries such as South Korea and China. Canine species were considered to be the new natural hosts for this virus. However, at the beginning of 2010, influenza-like respiratory signs, such as dyspnoea, were also observed among cats as well as in dogs in an animal shelter located in Seoul, South Korea. The affected cats showed 100 % morbidity and 40 % mortality. We were able to isolate a virus from a lung specimen of a dead cat, which had suffered from the respiratory disease, in embryonated-chicken eggs. The eight viral genes isolated were almost identical to those of the canine influenza H3N2 virus, suggesting interspecies transmission of canine influenza H3N2 virus to the cat. Moreover, three domestic cats infected with intranasal canine/Korea/GCVP01/07 (H3N2) all showed elevated rectal temperatures, nasal virus shedding and severe pulmonary lesions, such as suppurative bronchopneumonia. Our study shows, for the first time, that cats are susceptible to canine influenza H3N2 infection, suggesting that cats may play an intermediate host role in transmitting the H3N2 virus among feline and canine species, which could lead to the endemic establishment of the virus in companion animals. Such a scenario raises a public health concern, as the possibility of the emergence of new recombinant feline or canine influenza viruses in companion animals with the potential to act as a zoonotic infection cannot be excluded.

Genomic and protein structural maps of adaptive evolution of human influenza A virus to increased virulence in the mouse

Adaptive evolution is characterized by positive and parallel, or repeated selection of mutations. Mouse adaptation of influenza A virus (IAV) produces virulent mutants that demonstrate positive and parallel evolution of mutations in the hemagglutinin (HA) receptor and non-structural protein 1 (NS1) interferon antagonist genes. We now present a genomic analysis of all 11 genes of 39 mouse adapted IAV variants from 10 replicate adaptation experiments. Mutations were mapped on the primary and structural maps of each protein and specific mutations were validated with respect to virulence, replication, and RNA polymerase activity. Mouse adapted (MA) variants obtained after 12 or 20–21 serial infections acquired on average 5.8 and 7.9 nonsynonymous mutations per genome of 11 genes, respectively. Among a total of 115 nonsynonymous mutations, 51 demonstrated properties of natural selection including 27 parallel mutations. The greatest degree of parallel evolution occurred in the HA receptor and ribonucleocapsid components, polymerase subunits (PB1, PB2, PA) and NP. Mutations occurred in host nuclear trafficking factor binding sites as well as sites of virus-virus protein subunit interaction for NP, NS1, HA and NA proteins. Adaptive regions included cap binding and endonuclease domains in the PB2 and PA polymerase subunits. Four mutations in NS1 resulted in loss of binding to the host cleavage and polyadenylation specificity factor (CPSF30) suggesting that a reduction in inhibition of host gene expression was being selected. The most prevalent mutations in PB2 and NP were shown to increase virulence but differed in their ability to enhance replication and demonstrated epistatic effects. Several positively selected RNA polymerase mutations demonstrated increased virulence associated with >300% enhanced polymerase activity. Adaptive mutations that control host range and virulence were identified by their repeated selection to comprise a defined model for studying IAV evolution to increased virulence in the mouse.

Protecting animal and human health and the nation's food supply through veterinary diagnostic laboratory testing

The current detection system for animal diseases requires coordination between veterinarians; veterinary medical laboratories; and state, federal, and international agencies, as well as associated private sector industries. Veterinary clinical pathologists in clinical and governmental laboratories often have responsibilities and expertise in one or more laboratory disciplines involved in diagnosing zoonotic and/or emerging diseases and diseases exotic to the United States that are important to animal and human health and the nation's food supply. The knowledge and roles of all veterinary laboratory professionals are vital to detect, monitor, and confirm diseases and conditions that affect animal and human health and the nation's animal food supply.