Isolation of the pandemic (H1N1) 2009 virus and its reassortant with an H3N2 swine influenza virus from healthy weaning pigs in Thailand in 2011

Genetic Diversity of the Hemagglutinin Genes of Influenza a Virus in Asian Swine Populations

Swine influenza (SI) is a major respiratory disease of swine; SI is due to the influenza A virus of swine (IAV-S), a highly contagious virus with zoonotic potential. The intensity of IAV-S surveillance varies among countries because it is not a reportable disease and causes limited mortality in swine. Although Asia accounts for half of all pig production worldwide, SI is not well managed in those countries. Rigorously managing SI on pig farms could markedly reduce the economic losses, the likelihood of novel reassortants among IAV-S, and the zoonotic IAV-S infections in humans. Vaccination of pigs is a key control measure for SI, but its efficacy relies on the optimal antigenic matching of vaccine strains with the viral strains circulating in the field. Here, we phylogenetically reviewed the genetic diversity of the hemagglutinin gene among IAVs-S that have circulated in Asia during the last decade. This analysis revealed the existence of country-specific clades in both the H1 and H3 subtypes and cross-border transmission of IAVs-S. Our findings underscore the importance of choosing vaccine antigens for each geographic region according to both genetic and antigenic analyses of the circulating IAV-S to effectively manage SI in Asia.

Serological and molecular epidemiological study on swine influenza in Zambia

Influenza A viruses (IAVs) cause highly contagious respiratory diseases in humans and animals. In 2009, a swine-origin pandemic H1N1 IAV, designated A(H1N1)pdm09 virus, spread worldwide, and has since frequently been introduced into pig populations. Since novel reassortant IAVs with pandemic potential may emerge in pigs, surveillance for IAV in pigs is therefore necessary not only for the pig industry but also for public health. However, epidemiological information on IAV infection of pigs in Africa remains sparse. In this study, we collected 246 serum and 605 nasal swab samples from pigs in Zambia during the years 2011-2018. Serological analyses revealed that 49% and 32% of the sera collected in 2011 were positive for hemagglutination-inhibition (HI) and neutralizing antibodies against A(H1N1)pdm09 virus, respectively, whereas less than 5.3% of sera collected during the following period (2012-2018) were positive in both serological tests. The positive rate and the neutralization titres to A(H1N1)pdm09 virus were higher than those to classical swine H1N1 and H1N2 IAVs. On the other hand, the positive rate for swine H3N2 IAV was very low in the pig population in Zambia in 2011-2018 (5.3% and 0% in HI and neutralization tests, respectively). From nasal swab samples, we isolated one H3N2 and eight H1N1 IAV strains with an isolation rate of 1.5%. Phylogenetic analyses of all eight gene segments revealed that the isolated IAVs were closely related to human IAV strains belonging to A(H1N1)pdm09 and seasonal H3N2 lineages. Our findings indicate that reverse zoonotic transmission from humans to pigs occurred during the study period in Zambia and highlight the need for continued surveillance to monitor the status of IAVs circulating in swine populations in Africa.

Pathogenicity of novel reassortant Eurasian avian-like H1N1 influenza virus in pigs

Reassortant Eurasian avian-like (EA) H1N1 virus, possessing 2009 pandemic (pdm/09) and triple-reassortant (TR)-derived internal genes, namely G4 genotype, has replaced the G1 genotype EA H1N1 virus (all the genes were of EA origin) and become predominant in swine populations in China. Understanding the pathogenicity of G4 viruses in pigs is of great importance for disease control. Here, we conducted comprehensive analyses of replication and pathogenicity of G4 and G1 EA H1N1 viruses in pigs. G4 virus exhibited enhanced replication, increased duration of virus shedding, and caused more severe respiratory lesions in pigs compared with G1 virus. G4 virus, with viral ribonucleoprotein (vRNP) complex genes of pdm/09 origin, exhibited higher levels of nuclear accumulation and higher polymerase activity, which is essential for improved replication of G4 virus. These findings indicate that G4 virus poses a great threat to both swine industry and public health, and control measures should be urgently implemented.

Infection and risk factors of human and avian influenza in pigs in south China

The coinfection of swine influenza (SI) strains and avian/human-source influenza strains in piggeries can contribute to the evolution of new influenza viruses with pandemic potential. This study analyzed surveillance data on SI in south China and explored the spatial predictor variables associated with different influenza infection scenarios in counties within the study area. Blood samples were collected from 7670 pigs from 534 pig farms from 2015 to 2017 and tested for evidence of infection with influenza strains from swine, human and avian sources. The herd prevalences for EA H1N1, H1N1pdm09, classic H1N1, HS-like H3N2, seasonal human H1N1 and avian influenza H9N2 were 88.5, 64.5, 60.3, 57.8, 12.9 and 10.3 %, respectively. Anthropogenic factors including detection frequency, chicken density, duck density, pig density and human population density were found to be better predictor variables for three influenza infection scenarios (infection with human strains, infection with avian strains, and coinfection with H9N2 avian strain and at least one swine strain) than were meteorological and geographical factors. Predictive risk maps generated for the four provinces in south China highlighted that the areas with a higher risk of the three infection scenarios were predominantly clustered in the delta area of the Pearl River in Guangdong province and counties surrounding Poyang Lake in Jiangxi province. Identification of higher risk areas can inform targeted surveillance for influenza in humans and pigs, helping public health authorities in designing risk-based SI control strategies to address the pandemic influenza threat in south China.

Localization and immunohistochemical detection of swine influenza A virus subtype H1N1 antigen in formalin-fixed, paraffin-embedded lung tissues from naturally infected pigs

Background

Swine influenza A viruses (SIV) infection is among the leading causes of respiratory diseases in a number of animal species and human, and has been reported to cause substantial losses to pig industry. Previous reports of serological, molecular, and surveillance studies in commercial piggeries in Nigeria indicated the presence of SIV subtypes H1N1 and H3N2 in infected pigs; hitherto, there exists lack of studies on the pulmonary pathology and pathogenicity of SIV in Nigeria. This study investigates the presence of SIV subtype H1N1 antigen in the formalin-fixed paraffin-embedded lung sections obtained from apparently healthy pigs slaughtered at abattoirs located in Lagos, Ogun, and Oyo States, Southwest Nigeria using a streptavidin-biotin (ABC) immunoperoxidase (IP) staining. Two hundred four lungs consisting of 144 grossly pneumonic lungs and 60 apparently normal lungs were randomly collected, fixed in 10% neutral-buffered formalin, embedded in paraffin wax, and processed for histopathological examination and immunohistochemistry.

Results

The main gross lesions were marked pulmonary edema and mild bilateral consolidation of cranial lobes. Histopathology revealed suppurative bronchitis, and bronchiolitis with or without concurrent widespread degeneration and necrosis of epithelial cells (52.08%) and thickening of alveolar septa due to cellular infiltration consisting predominantly of neutrophils and mononuclear cells (macrophages and plasma cells) (39.58%). The lumina of most airways contained exudate consisting of neutrophils, desquamated epithelia cells, and necrotic debris. SIV antigen was immunohistochemically detected in 7/204 (3.43%) samples using SIV-specific (H1N1) monoclonal antibody. Positive cells exhibited a typical dark-brown reaction in the infected cells. A strong positive immunohistochemical staining was detected mainly in the alveolar macrophages and bronchial submucosal glandular epithelial cells while less intense staining was observed in the bronchiolar epithelial cells.

Conclusions

The present study describes the distribution and localization of SIV subtype H1N1 antigens in the lung tissues of the infected pigs and provides public awareness on the presence of the virus in pig population in Nigeria and the risk factors associated with the infection. Therefore, people working in pig farms should maintain high level of biosafety and personal hygiene. This is the first report of immunohistochemical detection of SIV subtype H1N1 antigen in naturally infected pigs in Nigeria and may indicate rapid dissemination of the virus in susceptible pigs in the study area. A further molecular epidemiological study to investigate other SIV subtypes circulating in Nigerian pig population is warranted.

Persistence of pdm2009-H1N1 internal genes of swine influenza in pigs, Thailand

Swine influenza is one of the important zoonotic diseases of pigs. We conducted a longitudinal survey of swine influenza A viruses (S-IAV) circulating in a pig farm with history of endemic S-IAV infection from 2017 to 2018. The samples were collected from 436 pigs including nasal swab samples (n = 436) and blood samples (n = 436). Our result showed that 18.81% (82/436) were positive for influenza A virus and subsequently 57 S-IAV could be isolated. Then 24 out of 57 S-IAVs were selected for whole genome sequencing and could be subtyped as S-IAV-H1N1 (n = 18) and S-IAV-H3N2 (n = 6). Of 24 S-IAVs, we observed 3 genotypes of S-IAVs including rH1N1 (pdm + 1), rH1N1 (pdm + 2), and rH3N2 (pdm + 2). Since all genotypes of S-IAVs in this study contained internal genes from pdmH1N1-2009, it could be speculated that pdmH1N1-2009 was introduced in a pig farm and then multiple reassorted with endemic S-IAVs to generate diversify S-IAV genotypes. Our study supported and added the evidences that pdmH1N1-2009 and it reassortant have predominately persisted in pig population in Thailand. Thus, monitoring of S-IAVs in pigs, farm workers and veterinarians in pig farms is important and should be routinely conducted.

Swine influenza virus: Current status and challenge

Since swine influenza virus was first isolated in 1930, it has become endemic in pigs worldwide. Although large amount of swine influenza vaccines has been used in swine industry, swine influenza still cannot be efficiently controlled and has been an important economic disease for swine industry. The high diversity and varied distribution of different subtypes and genotypes of swine influenza viruses circulating in pigs globally is a major challenge to produce broadly effective vaccines and control disease. Importantly, swine influenza virus is able to cross species barrier to infect humans and even caused influenza pandemic in 2009. Herein, current status and challenge of swine influenza viruses is reviewed and discussed.

Genetic Characterization of Influenza A Viruses in Japanese Swine in 2015 to 2019

Understanding the current status of influenza A viruses of swine (IAVs-S) and their evolution at the farm level is important for controlling these pathogens. Efforts to monitor IAVs-S during 2015 to 2019 yielded H1N1, H1N2, and H3N2 viruses. H1 genes in Japanese swine formed a unique clade in the classical swine H1 lineage of 1A.1, and H3 genes originating from 1999–2000 human seasonal influenza viruses appear to have become established among Japanese swine. A(H1N1)pdm09-derived H1 genes became introduced repeatedly and reassorted with endemic IAVs-S, resulting in various combinations of surface and internal genes among pig populations in Japan. At the farm level, multiple introductions of IAVs-S with phylogenetically distinct HA sequences occurred, or IAVs-S derived from a single introduction have persisted for at least 3 years with only a single mutation at the antigenic site of the HA protein. Continued monitoring of IAVs-S is necessary to update and maximize control strategies.

To assess the current status of influenza A viruses of swine (IAVs-S) throughout Japan and to investigate how these viruses persisted and evolve on pig farms, we genetically characterized IAVs-S isolated during 2015 to 2019. Nasal swab samples collected through active surveillance and lung tissue samples collected for diagnosis yielded 424 IAVs-S, comprising 78 H1N1, 331 H1N2, and 15 H3N2 viruses, from farms in 21 sampled prefectures in Japan. Phylogenetic analyses of surface genes revealed that the 1A.1 classical swine H1 lineage has evolved uniquely since the late 1970s among pig populations in Japan. During 2015 to 2019, A(H1N1)pdm09 viruses repeatedly became introduced into farms and reassorted with endemic H1N2 and H3N2 IAVs-S. H3N2 IAVs-S isolated during 2015 to 2019 formed a clade that originated from 1999–2000 human seasonal influenza viruses; this situation differs from previous reports, in which H3N2 IAVs-S derived from human seasonal influenza viruses were transmitted sporadically from humans to swine but then disappeared without becoming established within the pig population. At farms where IAVs-S were frequently isolated for at least 3 years, multiple introductions of IAVs-S with phylogenetically distinct hemagglutinin (HA) genes occurred. In addition, at one farm, IAVs-S derived from a single introduction persisted for at least 3 years and carried no mutations at the deduced antigenic sites of the hemagglutinin protein, except for one at the antigenic site (Sa). Our results extend our understanding regarding the status of IAVs-S currently circulating in Japan and how they genetically evolve at the farm level.

IMPORTANCE Understanding the current status of influenza A viruses of swine (IAVs-S) and their evolution at the farm level is important for controlling these pathogens. Efforts to monitor IAVs-S during 2015 to 2019 yielded H1N1, H1N2, and H3N2 viruses. H1 genes in Japanese swine formed a unique clade in the classical swine H1 lineage of 1A.1, and H3 genes originating from 1999–2000 human seasonal influenza viruses appear to have become established among Japanese swine. A(H1N1)pdm09-derived H1 genes became introduced repeatedly and reassorted with endemic IAVs-S, resulting in various combinations of surface and internal genes among pig populations in Japan. At the farm level, multiple introductions of IAVs-S with phylogenetically distinct HA sequences occurred, or IAVs-S derived from a single introduction have persisted for at least 3 years with only a single mutation at the antigenic site of the HA protein. Continued monitoring of IAVs-S is necessary to update and maximize control strategies.

A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide

The global anxiety and a significant threat to public health due to the current COVID-19 pandemic reiterate the need for active surveillance for the zoonotic virus diseases of pandemic potential. Influenza virus due to its wide host range and zoonotic potential poses such a significant threat to public health. Swine serve as a “mixing vessel” for influenza virus reassortment and evolution which as a result may facilitate the emergence of new strains or subtypes of zoonotic potential. In this context, the currently available scientific data hold a high significance to unravel influenza virus epidemiology and evolution. With this objective, the current systematic review summarizes the original research articles and case reports of all the four types of influenza viruses reported in swine populations worldwide. A total of 281 articles were found eligible through screening of PubMed and Google Scholar databases and hence were included in this systematic review. The highest number of research articles (n = 107) were reported from Asia, followed by Americas (n = 97), Europe (n = 55), Africa (n = 18), and Australia (n = 4). The H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were the most common influenza A virus subtypes reported in swine in most countries across the globe, however, few strains of influenza B, C, and D viruses were also reported in certain countries. Multiple reports of the avian influenza virus strains documented in the last two decades in swine in China, the United States, Canada, South Korea, Nigeria, and Egypt provided the evidence of interspecies transmission of influenza viruses from birds to swine. Inter-species transmission of equine influenza virus H3N8 from horse to swine in China expanded the genetic diversity of swine influenza viruses. Additionally, numerous reports of the double and triple-reassortant strains which emerged due to reassortments among avian, human, and swine strains within swine further increased the genetic diversity of swine influenza viruses. These findings are alarming hence active surveillance should be in place to prevent future influenza pandemics.

Syndromic survey and molecular analysis of influenza viruses at the human-swine interface in two West African cosmopolitan cities suggest the possibility of bidirectional interspecies transmission

Influenza viruses are frequently transmitted between pigs and their handlers, and among pig handlers. However, reports on socio-environmental variables as potential risk factors associated with transmission of influenza in West African swine production facilities are very scarce. Syndromic survey for influenza was therefore conducted in Ibadan, Nigeria, and Kumasi, Ghana, in order to identify and elucidate selected socio-environmental variables that may contribute to the occurrence and distribution of influenza-like illness (ILI) among swine industry workers. In addition, molecular analyses were conducted to elucidate the nature of influenza viruses circulating at the human-swine interface in these cities and better understand the dynamics of their transmission. Influenza viruses were detected by type-specific and subtype-specific RT-PCR. Sequencing and phylogenetic analyses were carried out. Socio-environmental variables were tested by both univariable and multivariable regression methods for significance at p < 0.05. Three risk factors for ILI were identified in each city. These included "frequency of visit of pig handler to pig pen or lairage" (Ibadan: risk ratio [RR] = 1.54, 95% confidence interval [CI] = 1.36-1.79, p = 0.02; Kumasi: RR = 1.28, 95% CI = 1.11-1.71, p = 0.01) and "pig handler's awareness about biosecurity measures" (Ibadan: RR = 7.09, 95% CI = 2.36-21.32, p < 0.001; Kumasi: RR = 4.84, 95% CI = 1.98-11.80, p < 0.001). Influenza A(H1N1)pdm09 viruses, with M genes closely related to those which circulated among pigs in the two cities during the same period, were detected among Nigerian and Ghanaian pig industry workers. These findings suggest the possibility of bidirectional transmission of influenza at the human-swine interface in these cities and underscore the need for more extensive molecular studies. Risk factors identified may assist in the control of human-to-human and human-to-swine transmission of influenza in the West African swine industry.

Genetic and antigenic dynamics of influenza A viruses of swine on pig farms in Thailand

Surveillance studies of influenza A virus of swine (IAV-S) have accumulated information regarding IAVs-S circulating in Thailand, but how IAVs-S evolve within a farm remains unclear. In the present study, we isolated 82 A(H1N1)pdm09 and 87 H3N2 viruses from four farms from 2011 through 2017. We then phylogenetically and antigenically analyzed the isolates to elucidate their evolution within each farm. Phylogenetic analysis demonstrated multiple introductions of A(H1N1)pdm09 viruses that resembled epidemic A(H1N1)pdm09 strains in humans in Thailand, and they reassorted with H3N2 viruses as well as other A(H1N1)pdm09 viruses. Antigenic analysis revealed that the viruses had acquired antigenic diversity either by accumulating substitutions in the hemagglutinin protein or through the introduction of IAV-S strains with different antigenicity. Our results, obtained through continuous longitudinal surveillance, revealed that IAV-S can be maintained on a pig farm over several years through the generation of antigenic diversity due to the accumulation of mutations, introduction of new strains, and reassortment events.

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.

Novel triple-reassortant influenza viruses in pigs, Guangxi, China

Considered a “mixing vessel” for influenza viruses, pigs can give rise to new influenza virus reassortants that can threaten humans. During our surveillance of pigs in Guangxi, China from 2013 to 2015, we isolated 11 H1N1 and three H3N2 influenza A viruses of swine origin (IAVs-S). Out of the 14, we detected ten novel triple-reassortant viruses, which contained surface genes (hemagglutinin and neuraminidase) from Eurasian avian-like (EA) H1N1 or seasonal human-like H3N2, matrix (M) genes from H1N1/2009 pandemic or EA H1N1, nonstructural (NS) genes from classical swine, and the remaining genes from H1N1/2009 pandemic. Mouse studies indicate that these IAVs-S replicate efficiently without prior adaptation, with some isolates demonstrating lethality. Notably, the reassortant EA H1N1 viruses with EA-like M gene have been reported in human infections. Further investigations will help to assess the potential risk of these novel triple-reassortant viruses to humans.

Reassortant H5N1 Avian Influenza Virus Bearing PB2 Gene From a 2009 Pandemic H1N1 Exhibits Increased Pathogenicity in Mice

Reassortment is a key driving force of the evolution and host adaptation of the influenza virus. A(H1N1)pdm2009 (pdm09), a novel H1N1 influenza viral subtype, caused a pandemic in 2009. The strain was established in pig herds and cocirculated with the highly pathogenic H5N1 avian influenza virus. The coexistence of pdm09 with H5N1 raises concerns that reassortment may cause the development of novel viral strains with unpredictable virulence. Given that the viral polymerase subunit PB2 is a determinant of host range and pathogenicity, and that the substantial amino acid differences in PB2 between pdm09 and H5N1, including positions 590/591 and 271, which are shown to play key roles in enhanced polymerase activity in mammalian host cells, we generated a reassortant virus containing PB2 derived from a pdm09 (A/Liaoning/1/2009, LN/09) to investigate if pdm09-derived PB2 can function in a heterologous avian virus isolate as an adaptive strategy, with H5N1 (A/duck/Hubei/hangmei01/2006, HM/06) as the backbone. We assessed the biological characteristics, including pathogenicity, replication, and polymerase activity, of the reassortant. Compared with HM/06 and LN/09, H5N1 hybrid virus containing PB2 from LN/09 exhibited significantly increased pathogenicity in mice and proliferation activity in mammalian cell lines, as well as markedly enhanced polymerase activity. Our results indicate that the coexistence of H5N1 and pdm09 may pose a great threat to public health through reassortment. Moreover, our results highlight the importance of monitoring the emergence of H5N1 reassortants containing pdm09-derived PB2.

Molecular detection of influenza A(H1N1)pdm09 viruses with M genes from human pandemic strains among Nigerian pigs, 2013-2015: implications and associated risk factors

In the post-pandemic period, influenza A(H1N1)pdm09 virus has been detected in swine populations in different parts of the world. This study was conducted to determine the presence and spatial patterns of this human pandemic virus among Nigerian pigs and identify associated risk factors. Using a two-stage stratified random sampling method, nasal swab specimens were obtained from pigs in Ibadan, Nigeria during the 2013-2014 and 2014-2015 influenza seasons, and the virus was detected by reverse transcriptase-polymerase chain reaction (RT-PCR). Purified RT-PCR products were sequenced in both directions, and sequences were aligned using MUSCLE. Phylogenetic analysis was conducted in MEGA6. Purely spatial scan statistics and a spatial lag regression model were used to identify spatial clusters and associated risk factors. The virus was detected in both seasons, with an overall prevalence of 8·7%. Phylogenetic analyses revealed that the M genes were similar to those of pandemic strains which circulated in humans prior to and during the study. Cluster analysis revealed a significant primary spatial cluster (RR = 4·71, LLR = 5·66, P = 0·0046), while 'hours spent with pigs (R 2 = 0·90, P = 0·0018)' and 'hours spent with pigs from different farms (R 2 = 0·91, P = 0·0001)' were identified as significant risk factors (P < 0·05). These findings reveal that there is considerable risk of transmission of the pandemic virus, either directly from pig handlers or through fomites, to swine herds in Ibadan, Nigeria. Active circulation of the virus among Nigerian pigs could enhance its reassortment with endemic swine influenza viruses. Campaigns for adoption of biosecurity measures in West African piggeries and abattoirs should be introduced and sustained in order to prevent the emergence of a new influenza epicentre in the sub-region.

Control of endemic swine flu persistence in farrow-to-finish pig farms: a stochastic metapopulation modeling assessment

Swine influenza viruses (swIAVs) are known to persist endemically in farrow-to-finish pig farms, leading to repeated swine flu outbreaks in successive batches of pigs at a similar age (mostly around 8 weeks of age). This persistence in European swine herds involves swIAVs from European lineages including H1_avN1, H1_huN2, H3N2, the 2009 H1N1 pandemic virus and their reassortants. The specific population dynamics of farrow-to-finish pig farms, the immune status of the animals at infection-time, the co-circulation of distinct subtypes leading to consecutive or concomitant infections have been evidenced as factors favouring swIAV persistence within herds. We developed a stochastic metapopulation model representing the co-circulation of two distinct swIAVs within a typical farrow-to-finish pig herd to evaluate the risk of reassortant viruses generation due to co-infection events. Control strategies related to herd management and/or vaccination schemes (batch-to-batch or mass vaccination of the sow herd and vaccination of growing pigs) were implemented to assess their relative efficacy regarding viral persistence. The overall probability of a co-infection event for France, possibly leading to reassortment, was evaluated to 16.8%. The export of consecutive piglets batches was identified as the most efficient measure facilitating swIAV infection fade-out. Although some vaccination schemes (batch-to-batch vaccination) had a beneficial effect in breeding sows by reducing the persistence of swIAVs within this subpopulation, none of vaccination strategies achieved swIAVs fade-out within the entire farrow-to-finish pig herd.

Influenza A Viruses of Swine (IAV-S) in Vietnam from 2010 to 2015: Multiple Introductions of A(H1N1)pdm09 Viruses into the Pig Population and Diversifying Genetic Constellations of Enzootic IAV-S

Active surveillance of influenza A viruses of swine (IAV-S) involving 262 farms and 10 slaughterhouses in seven provinces in northern and southern Vietnam from 2010 to 2015 yielded 388 isolates from 32 farms; these viruses were classified into H1N1, H1N2, and H3N2 subtypes. Whole-genome sequencing followed by phylogenetic analysis revealed that the isolates represented 15 genotypes, according to the genetic constellation of the eight segments. All of the H1N1 viruses were entirely A(H1N1)pdm09 viruses, whereas all of the H1N2 and H3N2 viruses were reassortants among 5 distinct ancestral viruses: H1 and H3 triple-reassortant (TR) IAV-S that originated from North American pre-2009 human seasonal H1, human seasonal H3N2, and A(H1N1)pdm09 viruses. Notably, 93% of the reassortant IAV-S retained M genes that were derived from A(H1N1)pdm09, suggesting some advantage in terms of their host adaptation. Bayesian Markov chain Monte Carlo analysis revealed that multiple introductions of A(H1N1)pdm09 and TR IAV-S into the Vietnamese pig population have driven the genetic diversity of currently circulating Vietnamese IAV-S. In addition, our results indicate that a reassortant IAV-S with human-like H3 and N2 genes and an A(H1N1)pdm09 origin M gene likely caused a human case in Ho Chi Minh City in 2010. Our current findings indicate that human-to-pig transmission as well as cocirculation of different IAV-S have contributed to diversifying the gene constellations of IAV-S in Vietnam.

IMPORTANCE

This comprehensive genetic characterization of 388 influenza A viruses of swine (IAV-S) isolated through active surveillance of Vietnamese pig farms from 2010 through 2015 provides molecular epidemiological insight into the genetic diversification of IAV-S in Vietnam after the emergence of A(H1N1)pdm09 viruses. Multiple reassortments among A(H1N1)pdm09 viruses and enzootic IAV-S yielded 14 genotypes, 9 of which carried novel gene combinations. The reassortants that carried M genes derived from A(H1N1)pdm09 viruses became predominant, replacing those of the IAV-S that had been endemic in Vietnam since 2011. Notably, one of the novel reassortants likely caused a human case in Vietnam. Given that Vietnam is the second-largest pig-producing country in Asia, continued monitoring of IAV-S is highly important from the viewpoints of both the swine industry and human public health.

Effect of herd size on subclinical infection of swine in Vietnam with influenza A viruses

Background

Influenza A viruses of swine (IAV-S) cause acute and subclinical respiratory disease. To increase our understanding of the etiology of the subclinical form and thus help prevent the persistence of IAV-S in pig populations, we conducted active virologic surveillance in Vietnam, the second-largest pig-producing country in Asia, from February 2010 to December 2013.

Results

From a total of 7034 nasal swabs collected from clinically healthy pigs at 250 farms and 10 slaughterhouses, we isolated 172 IAV-S from swine at the weaning and early-fattening stages. The isolation rate of IAV-S was significantly higher among pigs aged 3 weeks to 4.5 months than in older and younger animals. IAV-S were isolated from 16 large, corporate farms and 6 family-operated farms from among the 250 farms evaluated. Multivariate logistic regression analysis revealed that “having more than 1,000 pigs” was the most influential risk factor for IAV-S positivity. Farms affected by reassortant IAV-S had significantly larger pig populations than did those where A(H1N1)pdm09 viruses were isolated, thus suggesting that large, corporate farms serve as sites of reassortment events.

Conclusions

We demonstrate the asymptomatic circulation of IAV-S in the Vietnamese pig population. Raising a large number of pigs on a farm has the strongest impact on the incidence of subclinical IAV-S infection. Given that only some of the corporate farms surveyed were IAV-S positive, further active monitoring is necessary to identify additional risk factors important in subclinical infection of pigs with IAV-S in Vietnam.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-016-0844-z) contains supplementary material, which is available to authorized users.

Maternally Derived Immunity Extends Swine Influenza A Virus Persistence within Farrow-to-Finish Pig Farms: Insights from a Stochastic Event-Driven Metapopulation Model

Swine Influenza A Viruses (swIAVs) have been shown to persist in farrow-to-finish pig herds with repeated outbreaks in successive batches, increasing the risk for respiratory disorders in affected animals and being a threat for public health. Although the general routes of swIAV transmission (i.e. direct contact and exposure to aerosols) were clearly identified, the transmission process between batches is still not fully understood. Maternally derived antibodies (MDAs) were stressed as a possible factor favoring within-herd swIAV persistence. However, the relationship between MDAs and the global spread among the different subpopulations in the herds is still lacking. The aim of this study was therefore to understand the mechanisms induced by MDAs in relation with swIAV spread and persistence in farrow-to-finish pig herds. A metapopulation model has been developed representing the population dynamics considering two subpopulations—breeding sows and growing pigs—managed according to batch-rearing system. This model was coupled with a swIAV-specific epidemiological model, accounting for partial passive immunity protection in neonatal piglets and an immunity boost in re-infected animals. Airborne transmission was included by a between-room transmission rate related to the current prevalence of shedding pigs. Maternally derived partial immunity in piglets was found to extend the duration of the epidemics within their batch, allowing for efficient between-batch transmission and resulting in longer swIAV persistence at the herd level. These results should be taken into account in the design of control programmes for the spread and persistence of swIAV in swine herds.

PLC-γ1 is involved in the inflammatory response induced by influenza A virus H1N1 infection

We have previously reported that phosphoinositide-specific phospholipase γ1 (PLC-γ1) signaling is activated by influenza virus H1N1 infection and mediates efficient viral entry in human epithelial cells. In this study, we show that H1N1 also activates PLCγ-1 signaling in human promonocytic cell line -derived macrophages. Surprisingly, the activated PLCγ-1 signaling is not important for viral replication in macrophages, but is involved in the virus-induced inflammatory responses. PLC-γ1-specific inhibitor U73122 strongly inhibits the H1N1 virus-induced NF-κB signaling, blocking the up-regulation of TNF-α, IL-6, MIP-1α, and reactive oxidative species. In a positive feedback loop, IL-1β and TNF-α activate the PLCγ-1 signaling in both epithelial and macrophage cell lines. In summary, we have shown for the first time that the PLCγ-1 signaling plays an important role in the H1N1-induced inflammatory responses. Our study suggests that targeting the PLCγ-1 signaling is a potential antiviral therapy against H1N1 by inhibiting both viral replication and excessive inflammation.

Novel reassortant influenza viruses between pandemic (H1N1) 2009 and other influenza viruses pose a risk to public health

Influenza A virus (IAV) is characterized by eight single-stranded, negative sense RNA segments, which allows for gene reassortment among different IAV subtypes when they co-infect a single host cell simultaneously. Genetic reassortment is an important way to favor the evolution of influenza virus. Novel reassortant virus may pose a pandemic among humans. In history, three human pandemic influenza viruses were caused by genetic reassortment between avian, human and swine influenza viruses. Since 2009, pandemic (H1N1) 2009 (pdm/09 H1N1) influenza virus composed of two swine influenza virus genes highlighted the genetic reassortment again. Due to wide host species and high transmission of the pdm/09 H1N1 influenza virus, many different avian, human or swine influenza virus subtypes may reassert with it to generate novel reassortant viruses, which may result in a next pandemic among humans. So, it is necessary to understand the potential threat of current reassortant viruses between the pdm/09 H1N1 and other influenza viruses to public health. This study summarized the status of the reassortant viruses between the pdm/09 H1N1 and other influenza viruses of different species origins in natural and experimental conditions. The aim of this summarization is to facilitate us to further understand the potential threats of novel reassortant influenza viruses to public health and to make effective prevention and control strategies for these pathogens.

Co-infection of influenza A viruses of swine contributes to effective shuffling of gene segments in a naturally reared pig

Following the 2009 H1N1 pandemic, surveillance activities have been accelerated globally to monitor the emergence of novel reassortant viruses. However, the mechanism by which influenza A viruses of swine (IAV-S) acquire novel gene constellations through reassortment events in natural settings remains poorly understood. To explore the mechanism, we collected 785 nasal swabs from pigs in a farm in Thailand from 2011 to 2014. H3N2, H3N1, H1N1 and H1N2 IAVs-S were isolated from a single co-infected sample by plaque purification and showed a high degree of diversity of the genome. In particular, the H1N1 isolates, possessing a novel gene constellation previously unreported in Thailand, exhibited greater variation in internal genes than H3N2 IAVs-S. A pair of isolates, designated H3N2-B and H1N1-D, was determined to have been initially introduced to the farm. These results demonstrate that numerous IAVs-S with various gene constellations can be created in a single co-infected pig via reassortment.

Reassortant swine influenza viruses isolated in Japan contain genes from pandemic A(H1N1) 2009

In 2013, three reassortant swine influenza viruses (SIVs)-two H1N2 and one H3N2-were isolated from symptomatic pigs in Japan; each contained genes from the pandemic A(H1N1) 2009 virus and endemic SIVs. Phylogenetic analysis revealed that the two H1N2 viruses, A/swine/Gunma/1/2013 and A/swine/Ibaraki/1/2013, were reassortants that contain genes from the following three distinct lineages: (i) H1 and nucleoprotein (NP) genes derived from a classical swine H1 HA lineage uniquely circulating among Japanese SIVs; (ii) neuraminidase (NA) genes from human-like H1N2 swine viruses; and (iii) other genes from pandemic A(H1N1) 2009 viruses. The H3N2 virus, A/swine/Miyazaki/2/2013, comprised genes from two sources: (i) hemagglutinin (HA) and NA genes derived from human and human-like H3N2 swine viruses and (ii) other genes from pandemic A(H1N1) 2009 viruses. Phylogenetic analysis also indicated that each of the reassortants may have arisen independently in Japanese pigs. A/swine/Miyazaki/2/2013 were found to have strong antigenic reactivities with antisera generated for some seasonal human-lineage viruses isolated during or before 2003, whereas A/swine/Miyazaki/2/2013 reactivities with antisera against viruses isolated after 2004 were clearly weaker. In addition, antisera against some strains of seasonal human-lineage H1 viruses did not react with either A/swine/Gunma/1/2013 or A/swine/Ibaraki/1/2013. These findings indicate that emergence and spread of these reassortant SIVs is a potential public health risk.

Genetic diversity of swine influenza viruses in Thai swine farms, 2011-2014

The pig is known as a "mixing vessel" for influenza A viruses. The co-circulation of multiple influenza A subtypes in pig populations can lead to novel reassortant strains. For this study, swine influenza surveillance was conducted from September 2011 to February 2014 on 46 swine farms in Thailand. In total, 78 swine influenza viruses were isolated from 2,821 nasal swabs, and 12 were selected for characterization by whole genome sequencing. Our results showed that the co-circulation of swine influenza subtypes H1N1, H3N2, and H1N2 in Thai swine farms was observable throughout the 3 years of surveillance. Furthermore, we repeatedly found reassortant viruses between endemic swine influenza viruses and pandemic H1N1 2009. This observation suggests that there is significant and rapid evolution of swine influenza viruses in swine. Thus, continuous surveillance is critical for monitoring novel reassortant influenza A viruses in Thai swine populations.

Novel triple reassortant H1N2 influenza viruses bearing six internal genes of the pandemic 2009/H1N1 influenza virus were detected in pigs in China

BACKGROUND

The pandemic A/H1N1 influenza viruses emerged in both Mexico and the United States in March 2009, and were transmitted efficiently in the human population. Transmissions of the pandemic 2009/H1N1 virus from humans to poultry and other species of mammals were reported from several continents during the course of the 2009 H1N1 pandemic. Reassortant H1N1, H1N2, and H3N2 viruses containing genes of the pandemic 2009/H1N1 viruses appeared in pigs in some countries.

STUDY DESIGN

In winter of 2012, a total of 2600 nasal swabs were collected from healthy pigs in slaughterhouses located throughout 10 provinces in China. The isolated viruses were subjected to genetic and antigenic analysis. Two novel triple-reassortant H1N2 influenza viruses were isolated from swine in China in 2012, with the HA gene derived from Eurasian avian-like swine H1N1, the NA gene from North American swine H1N2, and the six internal genes from the pandemic 2009/H1N1 viruses. The two viruses had similar antigenic features and some significant changes in antigenic characteristics emerged when compared to the previously identified isolates.

CONCLUSION

We inferred that the novel reassortant viruses in China may have arisen from the accumulation of the three types of influenza viruses, which further indicates that swine herds serve as "mixing vessels" for influenza viruses. Influenza virus reassortment is an ongoing process, and our findings highlight the urgent need for continued influenza surveillance among swine herds.

Genomic reassortants of pandemic A (H1N1) 2009 virus and endemic porcine H1 and H3 viruses in swine in Japan

From 2010 to 2013 in Japan, we isolated 11 swine influenza viruses (SIVs) from pigs showing respiratory symptoms. Sequence and phylogenetic analyses showed that 6 H1N1 viruses originated from the pandemic (H1N1) 2009 (pdm 09) virus and the other 5 viruses were reassortants between SIVs and pdm 09 viruses, representing 4 genotypes. Two H1N2 viruses contained H1 and N2 genes originated from Japanese H1N2 SIV together with internal genes of pdm 09 viruses. Additionally, 1 H1N2 virus contained a further NP gene originating from Japanese H1N2 SIV. One H1N1 virus contained only the H1 gene originating from Japanese H1 SIV in a pdm 09 virus background. One H3N2 virus contained H3 and N2 genes originating from Japanese H3N2 SIV together with internal genes of pdm 09 virus. The results indicate that pdm 09 viruses are distributed widely in the Japanese swine population and that several reassortments with Japanese SIVs have occurred.

Assessing Potential Risks of Influenza A Virus Transmission at the Pig-Human Interface in Thai Small Pig Farms Using a Questionnaire Survey

Influenza A viruses pose a major public health threat worldwide, especially due to the potential for inter-species transmission. Farmers could be among the first people to be infected with a novel reassortant virus in a pig herd and may serve as a source of the virus for their communities. In this study, the pig production systems of smallholders in rural Thailand were examined to qualitatively evaluate the potential risks that may contribute to the spread of influenza A viruses. The investigation was based on questionnaire interviews regarding pig farmers' practices and trading activities. We found that extensive pig-human contacts, commingling of pigs and chickens and suboptimal biosecurity practices adopted by farmers and traders may constitute substantial risks for inter-species influenza virus transmission, thereby posing a threat to pig populations and human public health. The regular practices of using manure as field fertilizer, hiring boars from outside and trading activities could contribute to the potential spread of influenza viruses in the local community. To mitigate the potential risks of influenza A virus transmission and spread in the local community, it is recommended that appropriate public health strategies and disease prevention policies for farmers and traders should be developed including improving biosecurity, encouraging separation of animals raised on farms and minimizing the exposure between pigs and humans. Furthermore, surveillance systems for pig diseases should be targeted around the festival months, and on-farm identification of pigs should be promoted.

Virus-specific factors associated with zoonotic and pandemic potential

Influenza A is a highly contagious respiratory virus in constant evolution and represents a threat to both veterinary and human public health. IA viruses (IAVs) originate in avian reservoirs but may adapt to humans, either directly or through the spillover to another mammalian species, to the point of becoming pandemic. IAVs must successfully be able to (i) transmit from animal to human, (ii) interact with host cells, and (iii) transmit from human to human. The mechanisms by which viruses evolve, cause zoonotic infections, and adapt to a new host species are indeed complex and appear to be a heterogeneous collection of viral evolutionary events rather than a single phenomenon. Progress has been made in identifying some of the genetic markers mainly associated with virulence and transmission; this achievement has improved our knowledge of how to manage a pandemic event and of how to identify IAVs with pandemic potential. Early evidence of emerging viruses and surveillance of animal IAVs is made possible only by strengthening the collaboration between the public and veterinary health sectors.

Emerging Zoonoses in Domesticated Livestock of Southeast Asia

Southeast Asia, identified as one of the hotspot for emerging and reemerging diseases is an area of emerging market with doubling population size within the next few years. The livestock industry is growing rapidly to cater for the population need via intensification and various diversification methods. This article discusses a few relevant emerging and emerging zoonoses within the past two decades and highlights the impact of these diseases to the animal industry and public health in the region.

Swine influenza: clinical, serological, pathological, and virological cross-sectional studies in nine farms in Argentina

BACKGROUND

Influenza A viruses (IAV) are important pathogens responsible for economic losses in the swine industry and represent a threat to public health. In Argentina, clinical, pathological, and virological findings suggest that IAV infection is widespread among pig farms. In addition, several subtypes of IAV, such as pH1N1, H3N2, δ1H1N1, and δ2H1N2, have been reported.

OBJECTIVES

To evaluate the infection patterns of influenza virus in nine pig farms in Argentina.

METHODS

Clinical, serological, pathological, and virological cross-sectional studies were conducted.

RESULTS

Clinical and pathological results were characteristic of endemic influenza infection in eight of the nine farms studied. By rRT-PCR, six of the nine farms were positive to influenza. Five IAV were obtained. Genome analysis determined that four of the isolations were pH1N1 and that the remaining one was a reassortant human origin H3N2 virus containing pandemic internal genes. Serological results showed that all farms were positive to influenza A antibodies. Moreover, the hemagglutination inhibition test showed that infection with viruses containing HA's from different subtypes (pH1, δ1H1, δ2H1, and H3) is present among the farms studied and that coinfections with two or more subtypes were present in 80.5% of positive pigs.

CONCLUSIONS

Because vaccines against IAV are not licensed in Argentina, these results reflect the situation of IAV infection in non-vaccinated herds. This study provides more information about the circulation and characteristics of IAV in a poorly surveyed region. This study provides more data that will be used to evaluate the tools necessary to control this disease.

Dynamics of influenza A virus infections in permanently infected pig farms: evidence of recurrent infections, circulation of several swine influenza viruses and reassortment events

Concomitant infections by different influenza A virus subtypes within pig farms increase the risk of new reassortant virus emergence. The aims of this study were to characterize the epidemiology of recurrent swine influenza virus infections and identify their main determinants. A follow-up study was carried out in 3 selected farms known to be affected by repeated influenza infections. Three batches of pigs were followed within each farm from birth to slaughter through a representative sample of 40 piglets per batch. Piglets were monitored individually on a monthly basis for serology and clinical parameters. When a flu outbreak occurred, daily virological and clinical investigations were carried out for two weeks. Influenza outbreaks, confirmed by influenza A virus detection, were reported at least once in each batch. These outbreaks occurred at a constant age within farms and were correlated with an increased frequency of sneezing and coughing fits. H1N1 and H1N2 viruses from European enzootic subtypes and reassortants between viruses from these lineages were consecutively and sometimes simultaneously identified depending on the batch, suggesting virus co-circulations at the farm, batch and sometimes individual levels. The estimated reproduction ratio R of influenza outbreaks ranged between 2.5 [1.9-2.9] and 6.9 [4.1-10.5] according to the age at infection-time and serological status of infected piglets. Duration of shedding was influenced by the age at infection time, the serological status of the dam and mingling practices. An impaired humoral response was identified in piglets infected at a time when they still presented maternally-derived antibodies.

Emergence of H3N2pM-like and novel reassortant H3N1 swine viruses possessing segments derived from the A (H1N1)pdm09 influenza virus, Korea

Background

Human‐to‐swine transmission of the pandemic H1N1 2009 [A(H1N1)pdm09] virus in pig populations resulted in reassortment events with endemic swine influenza viruses worldwide.

Objective

We investigated whether A(H1N1)pdm09‐derived reassortant viruses are present in South Korea and sought to determine the pathogenic potential of the novel swine viruses.

Methods

Pig lung tissues were collected from commercially slaughtered pigs. Isolated swine influenza viruses were genetically analyzed and characterized in vitro and in vivo.

Results

We identified reassortant H3N2 (H3N2pM‐like) and H3N1 swine viruses containing A(H1N1)pdm09‐like segments in Korean pigs that are genetically closely related to strains recently detected in pigs and humans in North America. Although the H3N2pM‐like and novel H3N1 reassortants demonstrated efficient replication in mice and ferrets, all the H3N1 strains exhibited growth advantage over the representative H3N2pM‐like virus in human airway cells. Interestingly, A/swine/Korea/CY02‐07/2012(H3N1) and A/swine/Korea/CY03‐13/2012(H3N1) reassortants were more readily transmitted to respiratory‐droplet‐contact ferrets compared with the H3N2pM‐like (A/swine/Korea/CY02‐10/2012) isolate. Furthermore, serologic evaluation showed poor antigenicity to contemporary reference human seasonal H3N2 vaccine strains.

Conclusions

We report here for the first time the isolation of H3N2pM‐like viruses outside North America and of novel reassortant swine H3N1 viruses with A(H1N1)pdm09‐derived genes. Apart from further complicating the genetic diversity of influenza A viruses circulating in domestic pigs, our data also indicate that these strains could potentially pose threat to public health asserting the need for continuous virus monitoring in these ecologically important hosts.

Genetic characterization of Thai swine influenza viruses after the introduction of pandemic H1N1 2009

Pandemic H1N1 2009 (pH1N1), influenza virus containing triple reassortant internal genes (TRIG) from avian, human, and swine influenza viruses emerged in 2009 as a highly infectious virus that was able to be transmitted from humans to pigs. During June 2010-May 2012, influenza virus surveillance was conducted in Thai pig population. Twenty-three samples (1.75%) were successfully isolated from total of 1,335 samples. Interestingly, pH1N1 (7 isolates, 30.34%), reassortant pH1N1 (rH1N1) (1 isolate, 4.35%), Thai endemic H1N1 (enH1N1) (3 isolates, 13.04%), reassortant H3N2 with pH1N1 internal genes (rH3N2) (9 isolates, 39.13%), and reassortant H1N2 with pH1N1 internal genes (rH1N2) (3 isolates, 13.04%) were found. It should be noted that rH1N1, rH1N2, and rH3N2 viruses contained the internal genes of pH1N1 virus having a TRIG cassette descendant from the North American swine lineage. Although all isolates in this study were obtained from mild clinically sick pigs, the viruses were still highly infective and possibly may play an important role in human-animal interfacing transmission. In addition, the TRIG cassette may have an influence on antigenic shift resulting in emergence of novel viruses, as seen in this study. Continuing surveillance of influenza A natural hosts, particularly in pigs is necessary.

Prevalence and characterization of influenza viruses in diverse species in Los Llanos, Colombia

While much is known about the prevalence of influenza viruses in North America and Eurasia, their prevalence in birds and mammals in South America is largely unknown. To fill this knowledge gap and provide a baseline for future ecology and epidemiology studies, we conducted 2 years of influenza surveillance in the eastern plains (Los Llanos) region of Colombia. Real-time reverse transcriptase polymerase chain reaction (RT-PCR) identified influenza viruses in wild birds, domestic poultry, swine and horses. Prevalence ranged from 2.6% to 13.4% across species. Swine showed the highest prevalence and were infected primarily with 2009 pandemic H1N1 (pH1N1) viruses genetically related to those in humans. In addition, we isolated H5N2 viruses from two resident species of whistling ducks (genus Dendrocygna) that differed completely from previous South American isolates, instead genetically resembling North American wild bird viruses. Both strains caused low pathogenicity in chickens and mammals. The prevalence and subtype diversity of influenza viruses isolated from diverse species within a small area of Colombia highlights the need for enhanced surveillance throughout South America, including monitoring of the potential transmissibility of low-pathogenic H5N2 viruses from wild birds to domestic poultry and the emergence of reassortant viruses in domestic swine.