Infection Dynamics of Pandemic 2009 H1N1 Influenza Virus in a Two‐Site Swine Herd

Influenza A viruses are common causes of respiratory disease in pigs and can be transmitted among multiple host species, including humans. The current lack of published information on infection dynamics of influenza viruses within swine herds hinders the ability to make informed animal health, biosecurity and surveillance programme decisions. The objectives of this serial cross‐sectional study were to describe the infection dynamics of influenza virus in a two‐site swine system by estimating the prevalence of influenza virus in animal subpopulations at the swine breeding herd and describing the temporal pattern of infection in a selected cohort of growing pigs weaned from the breeding herd. Nasal swab and blood samples were collected at approximately 30‐day intervals from the swine breeding herd (Site 1) known to be infected with pandemic 2009 H1N1 influenza virus. Sows, gilts and neonatal pigs were sampled at each sampling event, and samples were tested for influenza virus genome using matrix gene RRT‐PCR. Influenza virus was detected in neonatal pigs, but was not detected in sow or gilt populations via RRT‐PCR. A virus genetically similar to that detected in the neonatal pig population at Site 1 was also detected at the wean‐to‐finish site (Site 2), presumably following transportation of infected weaned pigs. Longitudinal sampling of nasal swabs and oral fluids revealed that influenza virus persisted in the growing pigs at Site 2 for at least 69 days. The occurrence of influenza virus in neonatal pigs, but not breeding females, at Site 1 emphasizes the potential for virus maintenance in this dynamic subpopulation, the importance of including this subpopulation in surveillance programmes and the potential transport of influenza virus between sites via the movement of weaned pigs.     

Investigation into the Epidemiology of African Swine Fever Virus at the Wildlife – Domestic Interface of the Gorongosa National Park,Central Mozambique

An epidemiological study of African swine fever (ASF) was conducted between March 2006 and September 2007 in a rural area adjacent to the Gorongosa National park (GNP) located in the Central Mozambique. Domestic pigs and warthogs were sampled to determine the prevalence of antibodies against ASF virus and the salivary antigens of Ornithodoros spp. ticks, while ticks collected from pig pens were tested for the presence of ASFV. In addition, 310 framers were interviewed to gain a better understanding of the pig value chain and potential practices that could impact on the spread of the virus. The sero‐prevalence to ASFV was 12.6% on farms and 9.1% in pigs, while it reached 75% in warthogs. Approximately 33% of pigs and 78% of warthogs showed antibodies against salivary antigens of ticks. The differences in sero‐prevalence between farms close to the GNP, where there is greater chance for the sylvatic cycle to cause outbreaks, and farms located in the rest of the district, where pig to pig transmission is more likely to occur, were marginally significant. Ornithodoros spp. ticks were found in only 2 of 20 pig pens outside the GNP, and both pens had ticks testing positive for ASFV DNA. Interviews carried out among farmers indicated that biosecurity measures were mostly absent. Herd sizes were small with pigs kept in a free‐ranging husbandry system (65%). Only 1.6% of farmers slaughtered on their premises, but 51% acknowledged allowing visitors into their farms to purchase pigs. ASF outbreaks seemed to have a severe economic impact with nearly 36% of farmers ceasing pig farming for at least 1 year after a suspected ASF outbreak. This study provides the first evidence of the existence of a sylvatic cycle in Mozambique and confirms the presence of a permanent source of virus for the domestic pig value chain.     

Reoccurrence of Suspected Human‐to‐Turkey Transmission of H1N1 Pandemic 2009 Virus in Turkey Breeder Flocks in Ontario and Manitoba, 2016

Soon after the emergence of 2009 pandemic H1N1, the first outbreaks in breeder turkey operations were reported that implicated human‐to‐turkey transmission. In the spring of 2016, the reoccurrence of 2009 pandemic H1N1 lineage viruses infecting breeder turkey flocks in Ontario and Manitoba, Canada, also implicated human‐to‐turkey transmission. In addition to raising concerns over biosecurity and vaccine failures, these cases once again raise the issue of whether turkeys have the potential to act as a bridge species to generate novel influenza A virus reassortants with public health implications.     

Infection of pigs with African swine fever virus via ingestion of stable flies (Stomoxys calcitrans)

Within Eastern Europe, African swine fever virus (ASFV ) has unexpectedly spread to farms with high biosecurity. In an attempt to explain this process, pigs were allowed to ingest flies that had fed on ASFV ‐spiked blood, which had a realistic titre for an infected pig. Some of the pigs became infected with the virus. Thus, ingestion of blood‐sucking flies, having fed on ASFV ‐infected wild boar before entering stables, represents a potential route for disease transmission.     

Epidemiological Analysis of Influenza A Infection in Cambodian Pigs and Recommendations for Surveillance Strategies

This study analysed the available data of seroprevalence to human influenza viruses in pigs in Cambodia using generalized linear mixed models in order to improve understanding of factors underlying the spread of human influenza viruses in Cambodian pigs. The associations between seroprevalence against seasonal H1N1 influenza virus in pigs and the population density of humans and pigs were not significant. However, a positive association between anti‐H3 antibodies in pigs and the human population density was identified. In contrast, there was a negative association between seroprevalence of H3N2 in pigs and the pig population density. Our study has highlighted the difficulty in identifying epidemiological risk factors when a limited data set is used for analyses. We therefore provide recommendations on data collection for future epidemiological analyses that could be improved by collecting metadata related to the animals sampled. In addition, serosurveillance for influenza A viruses in pigs in high‐risk areas or at slaughterhouses is recommended in resource‐limited countries.     

Characteristics of the first H16N3 subtype influenza A viruses isolated in western China

The first documented avian influenza virus subtype H16N3 was isolated in 1975 and is currently detectable in many countries worldwide. However, the prevalence, biological characteristics and threat to humans of the avian influenza virus H16N3 subtype in China remain poorly understood. We performed avian influenza surveillance in major wild bird gatherings across the country from 2017 to 2019, resulting in the isolation of two H16N3 subtype influenza viruses. Phylogenetic analysis showed these viruses belong to the Eurasian lineage, and both viruses presented the characteristics of inter‐species reassortment. In addition, the two viruses exhibited limited growth capacity in MDCK and A549 cells. Receptor‐binding assays indicated that the two H16N3 viruses presented dual receptor‐binding profiles, being able to bind to both human and avian‐type receptors, where GBHG/NX/2/2018(H16N3) preferentially bound the avian‐type receptor, while GBHG/NX/1/2018(H16N3) showed greater binding to the human‐type receptor, even the mice virulence data showed the negative results. Segments from other species have been introduced into the H16N3 avian influenza virus, which may alter its pathogenicity and host tropism, potentially posing a threat to animal and human health in the future. Consequently, it is necessary to increase monitoring of the emergence and spread of avian influenza subtype H16N3 in wild birds.     

Influenza A Virus in Backyard Pigs and Poultry in Rural Cambodia

Surveillance of influenza virus in humans and livestock is critical, given the worldwide public health threats and livestock production losses. Livestock farming involving close proximity between humans, pigs and poultry is often practised by smallholders in low‐income countries and is considered an important driver of influenza virus evolution. This study determined the prevalence and genetic characteristics of influenza A virus (IAV) in backyard pigs and poultry in Cambodia. A total of 751 animals were tested by matrix gene‐based rRT‐PCR, and influenza virus was detected in 1.5% of sampled pigs, 1.4% of chickens and 1.0% of ducks, but not in pigeons. Full‐length genome sequencing confirmed triple reassortant H3N2 in all IAV‐positive pigs and various low pathogenic avian influenza subtypes in poultry. Phylogenetic analysis of the swine influenza viruses revealed that these had haemagglutinin and neuraminidase genes originating from human H3N2 viruses previously isolated in South‐East Asia. Phylogenetic analysis also revealed that several of the avian influenza subtypes detected were closely related to internal viral genes from highly pathogenic H5N1 and H9N2 formerly sequenced in the region. High sequence homology was likewise found with influenza A viruses circulating in pigs, poultry and wild birds in China and Vietnam, suggesting transboundary introduction and cocirculation of the various influenza subtypes. In conclusion, highly pathogenic subtypes of influenza virus seem rare in backyard poultry, but virus reassortment, involving potentially zoonotic and pandemic subtypes, appears to occur frequently in smallholder pigs and poultry. Increased targeted surveillance and monitoring of influenza circulation on smallholdings would further improve understanding of the transmission dynamics and evolution of influenza viruses in humans, pigs and poultry in the Mekong subregion and could contribute to limit the influenza burden.     

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Five novel H5N6 influenza viruses, including four highly pathogenic avian influenza viruses and one low pathogenic avian influenza virus, were isolated from migratory birds in Ningxia, China, in November 2017. To understand the genetic origination of the novel H5N6 virus, and the infectivity and pathogenicity of the four highly pathogenic avian influenza viruses in mammals, phylogeographic analyses and infection studies in mice were performed. The phylogenetic and phylogeographic analyses showed that the H5N6 isolates, which are closely related to the viruses from Korea, Japan and the Netherlands, originated from reassortant virus between H5N8 and HxN6 viruses from western Russia. The animal study revealed that the SBD‐87 isolate presented moderate virulence in mice, suggesting a potential public risk to humans and a potential threat to public health.     

A review of highly pathogenic avian influenza in birds, with an emphasis on Asian H5N1 and recommendations for prevention and control

Avian influenza is a disease of both veterinary and public health importance. Influenza A viruses infect a range of hosts, including humans, and can cause significant morbidity and mortality. These viruses have high genetic variability, and new strains develop through both mutation and reassortment. Modes of transmission as well as the location of viral shedding may differ both by host species and by viral strain. Clinical signs of influenza A virus infection in birds vary considerably depending on the viral subtype, environmental factors, and age, health status, and species of the bird and range from decreased egg production and gastrointestinal manifestations to nervous system disorders and respiratory signs. Most commonly, peracute death with minimal clinical disease is observed in poultry infected with a highly pathogenic avian influenza virus. There are various prevention and control strategies for avian influenza, including education, biosecurity, surveillance, culling of infected animals, and vaccination. These strategies will differ by institution and current federal regulations. Each institution should have an established biosecurity protocol that can be properly instituted. Lastly, human health precautions, such as proper hand hygiene, personal protective equipment, and employee health monitoring, are imperative for at-risk individuals.     

Understanding African Swine Fever infection dynamics in Sardinia using a spatially explicit transmission model in domestic pig farms

African swine fever virus (ASFV ) has been endemic in Sardinia since 1978, resulting in severe losses for local pig producers and creating important problems for the island's veterinary authorities. This study used a spatially explicit stochastic transmission model followed by two regression models to investigate the dynamics of ASFV spread amongst domestic pig farms, to identify geographic areas at highest risk and determine the role of different susceptible pig populations (registered domestic pigs, non‐registered domestic pigs [brado ] and wild boar) in ASF occurrence. We simulated transmission within and between farms using an adapted version of the previously described model known as Be‐FAST . Results from the model revealed a generally low diffusion of ASF in Sardinia, with only 24% of the simulations resulting in disease spread, and for each simulated outbreak on average only four farms and 66 pigs were affected. Overall, local spread (indirect transmission between farms within a 2 km radius through fomites) was the most common route of transmission, being responsible for 98.6% of secondary cases. The risk of ASF occurrence for each domestic pig farm was estimated from the spread model results and integrated in two regression models together with available data for brado and wild boar populations. There was a significant association between the density of all three populations (domestic pigs, brado , and wild boar) and ASF occurrence in Sardinia. The most significant risk factors were the high densities of brado (OR = 2.2) and wild boar (OR = 2.1). The results of both analyses demonstrated that ASF epidemiology and infection dynamics in Sardinia create a complex and multifactorial disease situation, where all susceptible populations play an important role. To stop ASF transmission in Sardinia, three main factors (improving biosecurity on domestic pig farms, eliminating brado practices and better management of wild boars) need to be addressed.     

Poultry trading behaviours in Vietnamese live bird markets as risk factors for avian influenza infection in chickens

Vietnamese poultry are host to co‐circulating subtypes of avian influenza viruses, including H5N1 and H9N2, which pose a great risk to poultry productivity and to human health. AIVs circulate throughout the poultry trade network in Vietnam, with live bird markets being an integral component to this network. Traders at LBMs exhibit a variety of trading practices, which may influence the transmission of AIVs. We identified trading practices that impacted on AIV prevalence in chickens marketed in northern Vietnamese LBMs. We generated sequencing data for 31 H9N2 and two H5N6 viruses. Viruses isolated in the same LBM or from chickens sourced from the same province were genetically closer than viruses isolated in different LBMs or from chickens sourced in different provinces. The position of a vendor in the trading network impacted on their odds of having AIV‐infected chickens. Being a retailer and purchasing chickens from middlemen was associated with increased odds of infection, whereas odds decreased if vendors purchased chickens directly from large farms. Odds of infection were also higher for vendors having a greater volume of ducks unsold per day. These results indicate how the spread of AIVs is influenced by the structure of the live poultry trading network.     

Assessing the Potential Role of Pigs in the Epidemiology of Ebola Virus in Uganda

Uganda has experienced 4 Ebola outbreaks since the discovery of the virus. Recent epidemiological work has shown pigs are hosts for Ebola viruses. Due to their high reproduction rates, rapid weight gain, potential to provide quick financial returns and rising demand for pork, pig production in Uganda has undergone massive expansion. The combination of pork sector growth supported by development programmes and Ebola virus risk prompted a foresight exercise using desk, interview and spatial methods. The study found that the lack of serological evidence for specific reservoir species, the number of human index cases unable to account for their source of infection, domestic pig habitat overlap with potential Ebola virus zoonotic host environments, reported interactions at the human–pig–wildlife interface that could support transmission, fever in pigs as a commonly reported problem by pig farmers and temporal correlation of outbreaks with peak pork consumption periods warrants further research into potential zoonotic transmission in Uganda from pigs.     

Avian flu (H5N1): its epidemiology, prevention, and implications for anesthesiology

Avian flu, influenza A subtype H5N1, is an emergent and virulent disease that poses a threat to the health and safety of the world community. Avian flu is 1 of more than 25 influenza A viruses that reside primarily in birds but also infect humans and other mammals. Avian flu is responsible for the current outbreak in Asia; H5N1 has now displayed probable human-to-human transmission; it could be a harbinger of a global epidemic. Anesthesiologists are exposed to a risk for infection when they are involved in airway instrumentation of infected patients. Given the evidence of emerging resistance to common antiviral agents used to treat H5N1 influenza virus and limited supply of H5N1 vaccine, prevention is our best protection. The following article will detail the virology and preventive public health practices for H5N1. This knowledge can also be used to define and prevent other yet unidentified infectious threats.     

Phylogeography of H5N1 avian influenza virus in Indonesia

Highly pathogenic avian influenza (HPAI ) viruses of the H5N1 subtype are a major concern to human and animal health in Indonesia. This study aimed to characterize transmission dynamics of H5N1 over time using novel Bayesian phylogeography methods to identify factors which have influenced the spread of H5N1 in Indonesia. We used publicly available hemagglutinin sequence data sampled between 2003 and 2016 to model ancestral state reconstruction of HPAI H5N1 evolution. We found strong support for H5N1 transmission routes between provinces in Java Island and inter‐island transmissions, such as between Nusa Tenggara and Kalimantan Islands, not previously described. The spread is consistent with wild bird flyways and poultry trading routes. H5N1 migration was associated with the regions of high chicken densities and low human development indices. These results can be used to inform more targeted planning of H5N1 control and prevention activities in Indonesia.     

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Influenza A (H1N1) viruses are distributed worldwide and pose a threat to public health. Swine, as a natural host and mixing vessel of influenza A (H1N1) virus, play a critical role in the transmission of this virus to humans. Furthermore, swine influenza A (H1N1) viruses have provided all eight genes or some genes to the genomes of influenza strains that historically have caused human pandemics. Hence, persistent surveillance of influenza A (H1N1) virus in swine herds could contribute to the prevention and control of this virus. Here, we report a novel reassortant influenza A (H1N1) virus generated by reassortment between 2009 pandemic H1N1 viruses and swine viruses. We also found that this virus is prevalent in swine herds in Shandong Province, eastern China. Our findings suggest that surveillance of the emergence of the novel reassortant influenza A (H1N1) virus in swine is imperative.     

Detection of reassortant avian influenza A (H11N9) virus in wild birds in China

Human infectious avian influenza virus (AIV) H7N9 emerged in China in 2013. The N9 gene of H7N9, which has the ability to cause death in humans, originated from an H11N9 influenza strain circulating in wild birds. To investigate the frequency and distribution of the N9 gene of the H11N9 and H7N9 influenza virus circulating in wild birds between 2006 and 2015, 35,604 samples were collected and tested. No H7N9 but four strains of the H11N9 subtype AIV were isolated, and phylogenetic analyses showed that the four H11N9 viruses were intra‐subtype and inter‐subtype reassortant viruses. A sequence analysis revealed that all six internal genes of A/wild bird/Anhui/L306/2014 (H11N9) originated from an H9N2 AIV isolated in Korea. The H9N2 strain, which is an inner gene donor reassorted with other subtypes, is a potential threat to poultry and even humans. It is necessary to increase monitoring of the emergence and spread of H11N9 AIV in wild birds.     

Analysis of Swine Movements in a Province in Northern Vietnam and Application in the Design of Surveillance Strategies for Infectious Diseases

While swine production is rapidly growing in South‐East Asia, the structure of the swine industry and the dynamic of pig movements have not been well‐studied. However, this knowledge is a prerequisite for understanding the dynamic of disease transmission in swine populations and designing cost‐effective surveillance strategies for infectious diseases. In this study, we assessed the farming and trading practices in the Vietnamese swine familial farming sector, which accounts for most pigs in Vietnam, and for which disease surveillance is a major challenge. Farmers from two communes of a Red River Delta Province (northern Vietnam) were interviewed, along with traders involved in pig transactions. Major differences in the trade structure were observed between the two communes. One commune had mainly transversal trades, that is between farms of equivalent sizes, whereas the other had pyramidal trades, that is from larger to smaller farms. Companies and large familial farrow‐to‐finish farms were likely to act as major sources of disease spread through pig sales, demonstrating their importance for disease control. Familial fattening farms with high pig purchases were at greater risk of disease introduction and should be targeted for disease detection as part of a risk‐based surveillance. In contrast, many other familial farms were isolated or weakly connected to the swine trade network limiting their relevance for surveillance activities. However, some of these farms used boar hiring for breeding, increasing the risk of disease spread. Most familial farms were slaughtering pigs at the farm or in small local slaughterhouses, making the surveillance at the slaughterhouse inefficient. In terms of spatial distribution of the trades, the results suggested that northern provinces were highly connected and showed some connection with central and southern provinces. These results are useful to develop risk‐based surveillance protocols for disease detection in the swine familial sector and to make recommendations for disease control.     

Potential routes for indirect transmission of African swine fever virus into domestic pig herds

Following its introduction into Georgia in 2007, African swine fever virus (ASFV) has become widespread on the European continent and in Asia. In many cases, the exact route of introduction into domestic pig herds cannot be determined, but most introductions are attributed to indirect virus transmission. In this review, we describe knowledge gained about different matrices that may allow introduction of the virus into pig herds. These matrices include uncooked pig meat, processed pig‐derived products, feed, matrices contaminated with the virus and blood‐feeding invertebrates. Knowledge gaps still exist, and both field studies and laboratory research are needed to enhance understanding of the risks for ASFV introductions, especially via virus‐contaminated materials, including bedding and feed, and via blood‐feeding, flying insects. Knowledge obtained from such studies can be applied to epidemiological risk assessments for the different transmission routes. Such assessments can be utilized to help predict the most effective biosecurity and control strategies.