Pandemic A/H1N1/2009 influenza virus in swine, Cameroon, 2010

Human Seasonal Influenza Viruses in Swine Workers in Lagos, Nigeria: Consequences for Animal and Public Health

The influenza A virus has been scarcely investigated in pigs in Africa, with rare detection prior to 2009. The spread of A(H1N1)pdm09 changed the epidemiology due to frequent human-to-swine transmission and the emergence of various new reassortants. This study therefore aimed at estimating the level of circulation and characterizing influenza A viruses at the interface between swine workers, who are crucial players in the inter-species transmission of influenza A viruses, and their animals in several farms in Nigeria, a hub for pig production in Africa. This cross-sectional study showed that 24.6% (58/236) of the pig serum samples collected in 2013-2014 had anti-influenza A antibodies in the absence of vaccination programs, but none of the pig swabs (n = 1193) were positive according to RT-qPCR. Viral RNA was detected in 0.9% (2/229) of swine workers sampled at their place of work, and the strains were characterized as A(H1N1)pdm09 and seasonal A(H3N2). Our results highlight that more awareness of swine workers regarding the consequences of reverse zoonosis for animal and public health is warranted. Annual vaccination and the wearing of masks when experiencing influenza-like symptoms would help decrease influenza inter-species transmission, while surveillance should be adequately supported for early detection.

Possible bidirectional human-swine and subsequent human-human transmission of influenza virus A(H1N1)/2009 in Japan

In 2019, sows at a swine farm in Japan showed influenza-like illness (ILI) shortly after contact with an employee that exhibited ILI. Subsequently, a veterinarian became sick shortly after examining the sows and was diagnosed with influenza A virus (IAV) infection. Then, her family also contracted the infection. Subsequently, Pandemic A(H1N1)2009 viruses were isolated from all samples obtained from the sows, veterinarian and her family. Whole-genome analysis of the isolates confirmed that the viruses belonged to the same lineage (6B.1A) and the genome sequences obtained from all of the isolates were almost identical to each other. Furthermore, an epidemiological survey revealed no contact between veterinarians or their families and influenza patients prior to the onset of illness. These results strongly indicated a case of bidirectional infection between humans and sows. At the same time, we found a few unique mutations in the IAV genomes corresponding to the host species. The mutations that occurred in the virus after it was transferred from the farm worker to the sows were not observed in the humans infected from the sows, probably as a result of the mutations reverting to the original nucleotides. These results demonstrate that the bidirectional transmission of IAV is a potential risk for the next pandemic outbreak due to the emergence of new mutant strains.

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.

Influenza A and D Viruses in Non-Human Mammalian Hosts in Africa: A Systematic Review and Meta-Analysis

We conducted a systematic review and meta-analysis to investigate the prevalence and current knowledge of influenza A virus (IAV) and influenza D virus (IDV) in non-human mammalian hosts in Africa. PubMed, Google Scholar, Wiley Online Library and World Organisation for Animal Health (OIE-WAHIS) were searched for studies on IAV and IDV from 2000 to 2020. Pooled prevalence and seroprevalences were estimated using the quality effects meta-analysis model. The estimated pooled prevalence and seroprevalence of IAV in pigs in Africa was 1.6% (95% CI: 0-5%) and 14.9% (95% CI: 5-28%), respectively. The seroprevalence of IDV was 87.2% (95% CI: 24-100%) in camels, 9.3% (95% CI: 0-24%) in cattle, 2.2% (95% CI: 0-4%) in small ruminants and 0.0% (95% CI: 0-2%) in pigs. In pigs, H1N1 and H1N1pdm09 IAVs were commonly detected. Notably, the highly pathogenic H5N1 virus was also detected in pigs. Other subtypes detected serologically and/or virologically included H3N8 and H7N7 in equids, H1N1, and H3N8 and H5N1 in dogs and cats. Furthermore, various wildlife animals were exposed to different IAV subtypes. For prudent mitigation of influenza epizootics and possible human infections, influenza surveillance efforts in Africa should not neglect non-human mammalian hosts. The impact of IAV and IDV in non-human mammalian hosts in Africa deserves further investigation.

Variation in the HA antigenicity of A(H1N1)pdm09-related swine influenza viruses

Since the influenza pandemic in 2009, the causative agent 'A(H1N1)pdm09 virus', has been circulating in both human and swine populations. Although phylogenetic analyses of the haemagglutinin (HA) gene segment have revealed broader genetic diversity of A(H1N1)pdm09-related swine influenza A viruses (swIAVs) compared with human A(H1N1)pdm09 viruses, it remains unclear whether the genetic diversity reflects the antigenic differences in HA. To assess the impact of the diversity of the HA gene of A(H1N1)pdm09-related swIAVs on HA antigenicity, we characterized 12 swIAVs isolated in Japan from 2013 to 2018. We used a ferret antiserum and a panel of anti-HA mouse monoclonal antibodies (mAbs) raised against an early A(H1N1)pdm09 isolate. The neutralization assay with the ferret antiserum revealed that five of the 12 swIAVs were significantly different in their HA antigenicity from the early A(H1N1)pdm09 isolate. The mAbs also showed differential neutralization patterns depending on the swIAV strains. In addition, the single amino acid substitution at position 190 of HA, which was found in one of the five antigenically different swIAVs but not in human isolates, was shown to be one of the critical determinants for the antigenic difference of swIAV HAs. Two potential N-glycosylation sites at amino acid positions 185 and 276 of the HA molecule were identified in two antigenically different swIAVs. These results indicated that the genetic diversity of HA in the A(H1N1)pdm09-related swIAVs is associated with their HA antigenic variation. Our findings highlighted the need for surveillance to monitor the emergence of swIAV antigenic variants with public health importance.

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.

Exposure of domestic swine to influenza A viruses in Ghana suggests unidirectional, reverse zoonotic transmission at the human-animal interface

Influenza A viruses (IAVs) have both zoonotic and anthroponotic potential and are of public and veterinary importance. Swine are intermediate hosts and 'mixing vessels' for generating reassortants, progenies of which may harbour pandemic propensity. Swine handlers are at the highest risk of becoming infected with IAVs from swine but there is little information on the ecology of IAVs at the human-animal interface in Africa. We analysed and characterized nasal and throat swabs from swine and farmers respectively, for IAVs using RT-qPCR, from swine farms in the Ashanti region, Ghana. Sera were also analysed for IAVs antibodies and serotyped using ELISA and HI assays. IAV was detected in 1.4% (n = 17/1,200) and 2.0% (n = 2/99) of swine and farmers samples, respectively. Viral subtypes H3N2 and H1N1pdm09 were found in human samples. All virus-positive swine samples were subtyped as H1N1pdm09 phylogenetically clustering closely with H1N1pdm09 that circulated among humans during the study period. Phenotypic markers that confer sensitivity to Oseltamivir were found. Serological prevalence of IAVs in swine and farmers by ELISA was 3.2% (n = 38/1,200) and 18.2% (n = 18/99), respectively. Human H1N1pdm09 and H3N2 antibodies were found in both swine and farmers sera. Indigenous swine influenza A viruses and/or antibodies were not detected in swine or farmers samples. Majority (98%, n = 147/150) of farmers reported of not wearing surgical mask and few (4%, n = 6) reported to wear gloves when working. Most (n = 74, 87.7%) farmers reported of working on the farm when experiencing influenza-like illness. Poor husbandry and biosafety practices of farmers could facilitate virus transmission across the human-swine interface. Farmers should be educated on the importance of good farm practices to mitigate influenza transmission at the human-animal interface.

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.

Systematic Review of Important Viral Diseases in Africa in Light of the 'One Health' Concept

Emerging and re-emerging viral diseases are of great public health concern. The recent emergence of Severe Acute Respiratory Syndrome (SARS) related coronavirus (SARS-CoV-2) in December 2019 in China, which causes COVID-19 disease in humans, and its current spread to several countries, leading to the first pandemic in history to be caused by a coronavirus, highlights the significance of zoonotic viral diseases. Rift Valley fever, rabies, West Nile, chikungunya, dengue, yellow fever, Crimean-Congo hemorrhagic fever, Ebola, and influenza viruses among many other viruses have been reported from different African countries. The paucity of information, lack of knowledge, limited resources, and climate change, coupled with cultural traditions make the African continent a hotspot for vector-borne and zoonotic viral diseases, which may spread globally. Currently, there is no information available on the status of virus diseases in Africa. This systematic review highlights the available information about viral diseases, including zoonotic and vector-borne diseases, reported in Africa. The findings will help us understand the trend of emerging and re-emerging virus diseases within the African continent. The findings recommend active surveillance of viral diseases and strict implementation of One Health measures in Africa to improve human public health and reduce the possibility of potential pandemics due to zoonotic viruses.

Infectious diseases dynamics in growing/finishing pigs in Southern Brazil (2005-2016)

ABSTRACT: This study aimed to determine the frequency and distribution of infectious diseases diagnosed through necropsy examination and histopathological analysis in growing/finishing pigs along 12 years (2005-2016) in Southern Brazil. We evaluated 1906 anatomopathological exams of pigs at growing/finishing phases, of which the infectious diseases corresponded to 75.6% of the cases (1,441/1,906). Porcine circovirus type 2 (PCV2) infections were the most frequent, accounting for 51.3% of the cases (739/1,441) with a higher frequency from 2005 to 2007, characterizing an epidemic distribution, with a gradual decline after 2008. Infectious diseases affecting the respiratory system were the second major cause with 30.1% of the cases. Among these, necrotizing bronchiolitis caused by swine Influenza (15.1%, 218/1,441) and bacterial pneumonia (15%, 216/1,441) were the main conditions. Influenza was mostly diagnosed from 2010 to 2013, accounting for 43.1% (167/387) of the cases. After this period, both respiratory infectious diseases were endemic. Digestive system infectious diseases accounted for 10.5% of the diagnoses (151/1,441), with the following main conditions: Salmonella spp. enterocolitis (43.7%, 66/151), Lawsonia spp. proliferative enteropathy (41.7%, 63/151), and Brachyspira spp. colitis (14.6%, 22/151). The latter had a higher incidence from 2012 to 2014 with all cases detected in this period. Polyserositis and bacterial meningitis represented, respectively, 5.8% (84/1,441) and 2.3% (33/1,441) of the cases diagnosed, with a constant endemic character.

Status and gaps of research on respiratory disease pathogens of swine in Africa

Over the last two decades, the pig population in Africa has grown rapidly, reflecting the increased adoption of pig production as an important economic activity. Of all species, pigs are likely to constitute a greater share of the growth in the livestock subsector. However, constraints such as respiratory infectious diseases cause significant economic losses to the pig industry worldwide. Compared to industrialized countries, the occurrence and impacts of respiratory diseases on pig production in Africa is under-documented. Hence, knowledge on prevalence and incidence of economically important swine respiratory pathogens in pigs in Africa is necessary to guide interventions for prevention and control. The purpose of this review was to document the current status of research on five important respiratory pathogens of swine in Africa to inform future research and interventions. The pathogens included were porcine reproductive and respiratory syndrome virus (PPRSv), porcine circovirus 2 (PCV2), Mycoplasma hyopneumoniae (M. hyopneumoniae), Actinobacillus pleuropneumoniae (APP) and swine influenza A viruses (IAV). For this review, published articles were obtained using Harzing's Publish or Perish software tool from GoogleScholar. Articles were also sourced from PubMed, ScienceDirect, FAO and OIE websites. The terms used for the search were Africa, swine or porcine, respiratory pathogens, M. hyopneumoniae, APP, PCV2, PPRSv, IAV, prevention and control. In all, 146 articles found were considered relevant, and upon further screening, only 85 articles were retained for the review. The search was limited to studies published from 2000 to 2019. Of all the studies that documented occurrence of the five respiratory pathogens, most were on IAV (48.4%, n = 15), followed by PCV2 (25.8%, n = 8), PPRSv (19.4%, n = 6), while only one study (3.2%, n = 1) reported APP and M. hyopneumoniae. This review highlights knowledge and information gaps on epidemiologic aspects as well as economic impacts of the various pathogens reported in swine in Africa, which calls for further studies.

Serological evidence of swine exposure to pandemic H1N1/2009 influenza A virus in Burkina Faso

Despite improvement of human and avian influenza surveillance, swine influenza surveillance in sub-Saharan Africa is scarce and pandemic preparedness is still deemed inadequate, including in Burkina Faso. This cross-sectional study therefore aimed to investigate the (past) exposure of pigs to influenza A viruses. Practices of people with occupational contacts with pigs and their knowledge on influenza A were investigated in order to formulate future prevention guidelines. In 2016-2017, pig nasopharyngeal swabs and sera were collected and screened for the presence of influenza virus by RT-PCR or of anti-influenza antibodies by competitive ELISA. Seropositive samples were further characterized in virus microneutralization assays against human and swine H1N1 virus strains. Nasopharyngeal swabs were obtained from people with occupational contact with pigs and screened similarly. Demographic data as well as practices related to their profession were recorded. No influenza A virus was detected in nasopharyngeal swabs in humans (n = 358) or in pigs (n = 600). Seroprevalence in pigs reached 6.8 % (41/600) and seropositive animals were found in 50.0 % of extensive settings (10/20) and 19.0 % of (semi-)intensive farms (4/21). All positive sera reacted against the pandemic H1N1/2009 strain, while seropositivity against two Eurasian avian-like and one American swine H1N1 strains and individual titers were lower. These results suggested exposure to pandemic H1N1/2009 virus and cross-reactivity to other H1N1 strains. Farmers with higher frequency of contact to pigs, absence of protective equipment and lack of knowledge on zoonoses are likely key players in driving human-to-swine virus transmission.

Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery

Prevailing agro-ecological conditions and intermingling of human and animals in intensive farms in urban and peri-urban areas in Africa favour cross species transmission of pathogens at the human-animal interface. However, molecular epidemiology studies of zoonotic swine influenza viruses in this region are limited. In this study, isolates of pandemic influenza virus (H1N1pdm09) obtained from pigs in Nigeria were fully sequenced. BLAST of swine influenza virus genes from Nigeria was carried out in GenBank and gene alignment was done using MEGA version 7. Maximum likelihood method (PhyML program) was used to determine gene evolutionary relationships with other viruses and phylogenetic trees were constructed to infer genomic clusters and relationship. Swine influenza viruses isolated and sequenced in this study were monophyletic and 99% congenetic with human isolates from Nigeria, Cameroon, Ghana and USA suggesting reverse zoonotic transmission from humans to pigs in intensive husbandry. A Q240R and S31N substitution among others were detected in the haemagglutinin and matrix genes, respectively, indicating potentials for mutations during interspecies co-mingling and transmission. The A/H1N1pdm09 viruses circulating in pigs that are also exposed to avian influenza in the same epidemiological zones could engender emergence of novel viruses with zoonotic or pandemic potential requiring enhanced surveillance and monitoring.

Detection of pandemic influenza A/H1N1/pdm09 virus among pigs but not in humans in slaughterhouses in Kenya, 2013-2014

Objective

We conducted four cross-sectional studies over 1 year among humans and pigs in three slaughterhouses in Central and Western Kenya (> 350 km apart) to determine infection and exposure to influenza A viruses. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from participants who reported acute respiratory illness (ARI) defined as fever, cough or running nose. Nasal swabs and blood samples were collected from pigs. Human NP/OP and pig nasal swabs were tested for influenza A virus by real-time reverse transcriptase polymerase chain reaction (PCR) and pig serum was tested for anti-influenza A antibodies by ELISA.

Results

A total of 288 participants were sampled, 91.3% of them being male. Fifteen (5.2%) participants had ARI but the nine swabs collected from them were negative for influenza A virus by PCR. Of the 1128 pigs sampled, five (0.4%) nasal swabs tested positive for influenza A/H1N1/pdm09 by PCR whereas 214 of 1082 (19.8%) serum samples tested for Influenza A virus antibodies. There was higher seroprevalence in colder months and among pigs reared as free-range. These findings indicate circulation of influenza A/H1N1/pdm09 among pigs perhaps associated with good adaptation of the virus to the pig population after initial transmission from humans to pigs.

Seroprevalence of influenza A virus in pigs and low risk of acute respiratory illness among pig workers in Kenya

Background

Influenza A viruses pose a significant risk to human health because of their wide host range and ability to reassort into novel viruses that can cause serious disease and pandemics. Since transmission of these viruses between humans and pigs can be associated with occupational and environmental exposures, we investigated the association between occupational exposure to pigs, occurrence of acute respiratory illness (ARI), and influenza A virus infection.

Methods

The study was conducted in Kiambu County, the county with the highest level of intensive small-scale pig farming in Kenya. Up to 3 participants (> 2 years old) per household from pig-keeping and non-pig-keeping households were randomly recruited and followed up in 2013 (Sept-Dec) and 2014 (Apr-Aug). Oropharyngeal (OP) and nasopharyngeal (NP) swabs were collected from participants with ARI at the time of study visit. For the animal study, nasal and oropharyngeal swabs, and serum samples were collected from pigs and poultry present in enrolled households. The human and animal swab samples were tested for viral nucleic acid by RT-PCR and sera by ELISA for antibodies. A Poisson generalized linear mixed-effects model was developed to assess the association between pig exposure and occurrence of ARI.

Results

Of 1137 human participants enrolled, 625 (55%) completed follow-up visits including 172 (27.5%) pig workers and 453 (72.5%) non-pig workers. Of 130 human NP/OP swabs tested, four (3.1%) were positive for influenza A virus, one pig worker, and three among non-pig workers. Whereas none of the 4462 swabs collected from pig and poultry tested positive for influenza A virus by RT-PCR, 265 of 4273 (6.2%) of the sera tested positive for virus antibodies by ELISA, including 11.6% (230/1990) of the pigs and 1.5% (35/2,283) of poultry. The cumulative incidence of ARI was 16.9% among pig workers and 26.9% among the non-pig workers. The adjusted risk ratio for the association between being a pig worker and experiencing an episode of ARI was 0.56 (95% CI [0.33, 0.93]), after adjusting for potential confounders.

Conclusions

Our findings demonstrate moderate seropositivity for influenza A virus among pigs, suggesting the circulation of swine influenza virus and a potential for interspecies transmission.

Adaptation of Human Influenza Viruses to Swine

A large diversity of influenza A viruses (IAV) within the H1N1/N2 and H3N2 subtypes circulates in pigs globally, with different lineages predominating in specific regions of the globe. A common characteristic of the ecology of IAV in swine in different regions is the periodic spillover of human seasonal viruses. Such human viruses resulted in sustained transmission in swine in several countries, leading to the establishment of novel IAV lineages in the swine host and contributing to the genetic and antigenic diversity of influenza observed in pigs. In this review we discuss the frequent occurrence of reverse-zoonosis of IAV from humans to pigs that have contributed to the global viral diversity in swine in a continuous manner, describe host-range factors that may be related to the adaptation of these human-origin viruses to pigs, and how these events could affect the swine industry.

Identification and characterization of influenza A viruses in selected domestic animals in Kenya, 2010-2012

BACKGROUND

Influenza A virus subtypes in non-human hosts have not been characterized in Kenya. We carried out influenza surveillance in selected domestic animals and compared the virus isolates with isolates obtained in humans during the same period.

METHODS

We collected nasal swabs from pigs, dogs and cats; oropharyngeal and cloacal swabs from poultry; and blood samples from all animals between 2010 and 2012. A standardized questionnaire was administered to farmers and traders. Swabs were tested for influenza A by rtRT-PCR, virus isolation and subtyping was done on all positive swabs. All sera were screened for influenza A antibodies by ELISA, and positives were evaluated by hemagglutination inhibition (HI). Full genome sequencing was done on four selected pig virus isolates.

RESULTS

Among 3,798 sera tested by ELISA, influenza A seroprevalence was highest in pigs (15.9%; 172/1084), 1.2% (3/258) in ducks, 1.4% (1/72) in cats 0.6% (3/467) in dogs, 0.1% (2/1894) in chicken and 0% in geese and turkeys. HI testing of ELISA-positive pig sera showed that 71.5% had positive titers to A/California/04/2009(H1N1). Among 6,289 swabs tested by rRT-PCR, influenza A prevalence was highest in ducks [1.2%; 5/423] and 0% in cats and turkeys. Eight virus isolates were obtained from pig nasal swabs collected in 2011 and were determined to be A(H1N1)pdm09 on subtyping. On phylogenetic analysis, four hemagglutinin segments from pig isolates clustered together and were closely associated with human influenza viruses that circulated in Kenya in 2011.

CONCLUSION

Influenza A(H1N1)pdm09 isolated in pigs was genetically similar to contemporary human pandemic influenza virus isolates. This suggest that the virus was likely transmitted from humans to pigs, became established and circulated in Kenyan pig populations during the study period. Minimal influenza A prevalence was observed in the other animals studied.

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.

Transmission dynamics of pandemic influenza A(H1N1)pdm09 virus in humans and swine in backyard farms in Tumbes, Peru

Objectives

We aimed to determine the frequency of pH1N1 transmission between humans and swine on backyard farms in Tumbes, Peru.

Design

Two‐year serial cross‐sectional study comprising four sampling periods: March 2009 (pre‐pandemic), October 2009 (peak of the pandemic in Peru), April 2010 (1st post‐pandemic period), and October 2011 (2nd post‐pandemic period).

Sample

Backyard swine serum, tracheal swabs, and lung sample were collected during each sampling period.

Main outcome measures

We assessed current and past pH1N1 infection in swine through serological testing, virus culture, and RT‐PCR and compared the results with human incidence data from a population‐based active surveillance cohort study in Peru.

Results

Among 1303 swine sampled, the antibody prevalence to pH1N1 was 0% pre‐pandemic, 8% at the peak of the human pandemic (October 2009), and 24% in April 2010 and 1% in October 2011 (post‐pandemic sampling periods). Trends in swine seropositivity paralleled those seen in humans in Tumbes. The pH1N1 virus was isolated from three pigs during the peak of the pandemic. Phylogenetic analysis revealed that these viruses likely represent two separate human‐to‐swine transmission events in backyard farm settings.

Conclusions

Our findings suggest that human‐to‐swine pH1N1 transmission occurred during the pandemic among backyard farms in Peru, emphasizing the importance of interspecies transmission in backyard pig populations. Continued surveillance for influenza viruses in backyard farms is warranted.

Sentinel surveillance for influenza among severe acute respiratory infection and acute febrile illness inpatients at three hospitals in Ghana

Background

Influenza epidemiology in Africa is generally not well understood. Using syndrome definitions to screen patients for laboratory confirmation of infection is an established means to effectively conduct influenza surveillance.

Methods

To compare influenza‐related epidemiologic data, from October 2010 through March 2013, we enrolled hospitalized severe acute respiratory infection (SARI; fever with respiratory symptoms) and acute febrile illness (AFI; fever without respiratory or other localizing symptoms) patients from three referral hospitals in Ghana. Demographic and epidemiologic data were obtained from enrolled patients after which nasopharyngeal and oropharyngeal swabs were collected, and processed by molecular methods for the presence of influenza viruses.

Results

Of 730 SARI patients, 59 (8%) were influenza positive; of 543 AFI patients, 34 (6%) were positive for influenza. Both SARI and AFI surveillance yielded influenza A(H3N2) (3% versus 1%), A(H1N1)pdm09 (2% versus 1%), and influenza B (3% versus 4%) in similar proportions. Data from both syndromes show year‐round influenza transmission but with increased caseloads associated with the rainy seasons.

Conclusions

As an appreciable percentage of influenza cases (37%) presented without defined respiratory symptoms, and thus met the AFI but not the SARI definition, it is important to consider broader screening criteria (i.e., AFI) to identify all laboratory‐confirmed influenza. The identified influenza transmission seasonality has important implications for the timing of related public health interventions.

The global antigenic diversity of swine influenza A viruses

Swine influenza presents a substantial disease burden for pig populations worldwide and poses a potential pandemic threat to humans. There is considerable diversity in both H1 and H3 influenza viruses circulating in swine due to the frequent introductions of viruses from humans and birds coupled with geographic segregation of global swine populations. Much of this diversity is characterized genetically but the antigenic diversity of these viruses is poorly understood. Critically, the antigenic diversity shapes the risk profile of swine influenza viruses in terms of their epizootic and pandemic potential. Here, using the most comprehensive set of swine influenza virus antigenic data compiled to date, we quantify the antigenic diversity of swine influenza viruses on a multi-continental scale. The substantial antigenic diversity of recently circulating viruses in different parts of the world adds complexity to the risk profiles for the movement of swine and the potential for swine-derived infections in humans.

DOI:http://dx.doi.org/10.7554/eLife.12217.001

Influenza viruses, commonly called flu, infect millions of people and animals every year and occasionally causes pandemics in humans. The immune system can neutralise flu viruses by recognising the proteins on the virus surface, generically referred to as antigens. These antigens change as flu viruses evolve to escape detection by the immune system. These changes tend to be relatively small such that exposure to one flu virus generates immunity that is still effective against other related flu viruses. However, over time, the accumulation of these small changes can result in larger differences such that prior infections no longer provide protection against the new virus.

Influenza A viruses infect a wide variety of birds and mammals. Viruses can also transmit from one species to another, which may result in the introduction of viruses with antigens that are new to the recipient species and which have the potential to cause substantial outbreaks. Pig flu viruses have long been considered to be a potential risk for human pandemic viruses and were the source of the 2009 pandemic H1N1 virus. Importantly, humans often transmit flu viruses to pigs. Understanding the dynamics and consequences of this two-way transmission is important for designing effective strategies to detect and respond to new strains of flu.

Influenza A viruses of the H1 and H3 subtypes circulate widely in pigs. However, it was poorly understood how closely related swine and human viruses circulating in different regions were to one another and how much the antigens varied between the different viruses.

Lewis, Russell et al. have now analysed the antigenic variation of hundreds of H1 and H3 viruses from pigs on multiple continents. The antigenic diversity of recent swine flu viruses resembles the diversity of H1 and H3 viruses observed in humans over the last 40 years. A key factor driving the diversity of the H1 and H3 viruses in pigs is the frequent introduction of human viruses to pigs. In contrast, only one flu virus from a bird had contributed to the observed antigenic diversity in pigs in a substantial way.

Once in pigs, human-derived flu viruses continue to evolve their antigens. This results in a tremendous diversity of flu viruses that can be transmitted to other pigs and also to humans. These flu viruses could pose a serious risk to public health because they are no longer similar to the current human flu strains. These findings have important implications not only for developing flu vaccines for pigs but also for informing the development of more-effective surveillance and disease-control strategies to prevent the spread of new flu variants.

DOI:http://dx.doi.org/10.7554/eLife.12217.002

Influenza A Viruses of Human Origin in Swine, Brazil

Multiple divergent lineages challenge the design of cross-protective vaccines and highlight the need for additional surveillance.

The evolutionary origins of the influenza A(H1N1)pdm09 virus that caused the first outbreak of the 2009 pandemic in Mexico remain unclear, highlighting the lack of swine surveillance in Latin American countries. Although Brazil has one of the largest swine populations in the world, influenza was not thought to be endemic in Brazil’s swine until the major outbreaks of influenza A(H1N1)pdm09 in 2009. Through phylogenetic analysis of whole-genome sequences of influenza viruses of the H1N1, H1N2, and H3N2 subtypes collected in swine in Brazil during 2009–2012, we identified multiple previously uncharacterized influenza viruses of human seasonal H1N2 and H3N2 virus origin that have circulated undetected in swine for more than a decade. Viral diversity has further increased in Brazil through reassortment between co-circulating viruses, including A(H1N1)pdm09. The circulation of multiple divergent hemagglutinin lineages challenges the design of effective cross-protective vaccines and highlights the need for additional surveillance.

Novel Human-like Influenza A Viruses Circulate in Swine in Mexico and Chile

INTRODUCTION

Further understanding of the genetic diversity and evolution of influenza A viruses circulating in swine (IAV-S) is important for the development of effective vaccines and our knowledge of pandemic threats. Until recently, very little was known of IAV-S diversity in Latin America, owing to a lack of surveillance.

METHODS

To address this gap, we sequenced and conducted a phylogenetic analysis of 69 hemagglutinin (HA) sequences from IAV-S isolates collected in swine in Mexico and Chile during 2010-2014, including the H1N1, H1N2, and H3N2 subtypes.

RESULTS

Our analysis identified multiple IAV-S lineages that appear to have been circulating undetected in swine for decades, including four novel IAV-S lineages of human seasonal virus origin that have not been previously identified in any swine populations globally. We also found evidence of repeated introductions of pandemic H1N1 viruses from humans into swine in Mexico and Chile since 2009, and incursions of H1 and H3 viruses from North American swine into Mexico.

DISCUSSION

Overall, our findings indicate that at least 12 genetically distinct HA lineages circulate in Latin American swine herds, only two of which have been found in North American swine herds. Human-to-swine transmission, spatial migration via swine movements, and genomic reassortment are the key evolutionary mechanisms that generate this viral diversity. Additional antigenic characterization and whole-genome sequencing is greatly needed to understand the diversity and independent evolution of IAV-S in Latin America.

Influenza A(H1N1)pdm09 virus in pigs, Togo, 2013

We collected 325 nasal swabs from freshly slaughtered previously healthy pigs from October 2012 through January 2014 in a slaughterhouse near Lomé in Togo. Influenza A virus genome was detected by RT-PCR in 2.5-12.3% of the pooled samples, and results of hemagglutinin subtyping RT-PCR assays showed the virus in all the positive pools to be A(H1N1)pdm09. Virus was isolated on MDCK cells from a representative specimen, A/swine/Togo/ONA32/2013(H1N1). The isolate was fully sequenced and harbored eight genes similar to A(H1N1)pdm09 virus genes circulating in humans in 2012-2013, suggesting human-to-swine transmission of the pathogen.

Control of a Reassortant Pandemic 2009 H1N1 Influenza Virus Outbreak in an Intensive Swine Breeding Farm: Effect of Vaccination and Enhanced Farm Management Practices

Influenza A viruses in swine cause considerable economic losses and raise concerns about their zoonotic potential. The current paucity of thorough empirical assessments of influenza A virus infection levels in swine herds under different control interventions hinders our understanding of their effectiveness. Between 2012 and 2013, recurrent outbreaks of respiratory disease caused by a reassortant pandemic 2009 H1N1 (H1N1pdm) virus were registered in a swine breeding farm in North-East Italy, providing the opportunity to assess an outbreak response plan based on vaccination and enhanced farm management. All sows/gilts were vaccinated with a H1N1pdm-specific vaccine, biosecurity was enhanced, weaning cycles were lengthened, and cross-fostering of piglets was banned. All tested piglets had maternally-derived antibodies at 30 days of age and were detectable in 5.3% of ~90 day-old piglets. There was a significant reduction in H1N1pdm RT-PCR detections after the intervention. Although our study could not fully determine the extent to which the observed trends in seropositivity or RT-PCR positivity among piglets were due to the intervention or to the natural course of the disease in the herd, we provided suggestive evidence that the applied measures were useful in controlling the outbreak, even without an all-in/all-out system, while keeping farm productivity at full.

Continual Reintroduction of Human Pandemic H1N1 Influenza A Viruses into Swine in the United States, 2009 to 2014

The diversity of influenza A viruses in swine (swIAVs) presents an important pandemic threat. Knowledge of the human-swine interface is particularly important for understanding how viruses with pandemic potential evolve in swine hosts. Through phylogenetic analysis of contemporary swIAVs in the United States, we demonstrate that human-to-swine transmission of pandemic H1N1 (pH1N1) viruses has occurred continuously in the years following the 2009 H1N1 pandemic and has been an important contributor to the genetic diversity of U.S. swIAVs. Although pandemic H1 and N1 segments had been largely removed from the U.S. swine population by 2013 via reassortment with other swIAVs, these antigens reemerged following multiple human-to-swine transmission events during the 2013-2014 seasonal epidemic. These findings indicate that the six internal gene segments from pH1N1 viruses are likely to be sustained long term in the U.S. swine population, with periodic reemergence of pandemic hemagglutinin (HA) and neuraminidase (NA) segments in association with seasonal pH1N1 epidemics in humans. Vaccinating U.S. swine workers may reduce infection of both humans and swine and in turn limit the role of humans as sources of influenza virus diversity in pigs.

IMPORTANCE

Swine are important hosts in the evolution of influenza A viruses with pandemic potential. Here, we analyze influenza virus sequence data generated by the U.S. Department of Agriculture's national surveillance system to identify the central role of humans in the reemergence of pandemic H1N1 (pH1N1) influenza viruses in U.S. swine herds in 2014. These findings emphasize the important role of humans as continuous sources of influenza virus diversity in swine and indicate that influenza viruses with pandemic HA and NA segments are likely to continue to reemerge in U.S. swine in association with seasonal pH1N1 epidemics in humans.

Global migration of influenza A viruses in swine

The complex and unresolved evolutionary origins of the 2009 H1N1 influenza pandemic exposed major gaps in our knowledge of the global spatial ecology and evolution of influenza A viruses in swine (swIAVs). Here we undertake an expansive phylogenetic analysis of swIAV sequence data and demonstrate that the global live swine trade strongly predicts the spatial dissemination of swIAVs, with Europe and North America acting as sources of viruses in Asian countries. In contrast, China has the world’s largest swine population but is not a major exporter of live swine, and is not an important source of swIAVs in neighboring Asian countries or globally. A meta-population simulation model incorporating trade data predicts that the global ecology of swIAVs is more complex than previously thought, and the US and China’s large swine populations are unlikely to be representative of swIAV diversity in their respective geographic regions, requiring independent surveillance efforts throughout Latin America and Asia.

Reverse zoonosis of influenza to swine: new perspectives on the human-animal interface

The origins of the 2009 influenza A (H1N1) pandemic in swine are unknown, highlighting gaps in our understanding of influenza A virus (IAV) ecology and evolution. We review how recently strengthened influenza virus surveillance in pigs has revealed that influenza virus transmission from humans to swine is far more frequent than swine-to-human zoonosis, and is central in seeding swine globally with new viral diversity. The scale of global human-to-swine transmission represents the largest 'reverse zoonosis' of a pathogen documented to date. Overcoming the bias towards perceiving swine as sources of human viruses, rather than recipients, is key to understanding how the bidirectional nature of the human-animal interface produces influenza threats to both hosts.

Serological evidence of pandemic (H1N1) 2009 virus in pigs, West and Central Africa

Besides birds, pigs are another important reservoir of influenza A viruses that can be transmitted to human, as highlighted by the emergence and spread of the pandemic (H1N1) virus (pdm/09) in 2009. Surveillance in pigs is therefore necessary for public health and influenza pandemic preparedness. Nevertheless, there is a serious lack of data on influenza in Africa, especially in swine. We therefore collected serum samples from pigs in Nigeria (2009, 2012) and Cameroon (2011) in which the presence of anti-influenza A neutralizing antibodies was investigated. Our serological survey suggests that, before the 2009 pandemic, only rare swine and human H3N2 or human H1N1 infections occurred in Nigeria in swine. However, in 2011-2012, 27.4% of pigs in Nigeria and 5.6% in Cameroon had antibodies against H1N1 viruses. Higher antibody titres against pdm/09 suggested that pigs were exposed to this or a similar virus, either by multiple introductions or sustained circulation, and that reactivity against American and European swine H1N1 viruses resulted from cross-reaction.

Introductions and evolution of human-origin seasonal influenza a viruses in multinational swine populations

The capacity of influenza A viruses to cross species barriers presents a continual threat to human and animal health. Knowledge of the human-swine interface is particularly important for understanding how viruses with pandemic potential evolve in swine hosts. We sequenced the genomes of 141 influenza viruses collected from North American swine during 2002 to 2011 and identified a swine virus that possessed all eight genome segments of human seasonal A/H3N2 virus origin. A molecular clock analysis indicates that this virus--A/sw/Saskatchewan/02903/2009(H3N2)--has likely circulated undetected in swine for at least 7 years. For historical context, we performed a comprehensive phylogenetic analysis of an additional 1,404 whole-genome sequences from swine influenza A viruses collected globally during 1931 to 2013. Human-to-swine transmission occurred frequently over this time period, with 20 discrete introductions of human seasonal influenza A viruses showing sustained onward transmission in swine for at least 1 year since 1965. Notably, human-origin hemagglutinin (H1 and H3) and neuraminidase (particularly N2) segments were detected in swine at a much higher rate than the six internal gene segments, suggesting an association between the acquisition of swine-origin internal genes via reassortment and the adaptation of human influenza viruses to new swine hosts. Further understanding of the fitness constraints on the adaptation of human viruses to swine, and vice versa, at a genomic level is central to understanding the complex multihost ecology of influenza and the disease threats that swine and humans pose to each other.

IMPORTANCE

The swine origin of the 2009 A/H1N1 pandemic virus underscored the importance of understanding how influenza A virus evolves in these animals hosts. While the importance of reassortment in generating genetically diverse influenza viruses in swine is well documented, the role of human-to-swine transmission has not been as intensively studied. Through a large-scale sequencing effort, we identified a novel influenza virus of wholly human origin that has been circulating undetected in swine for at least 7 years. In addition, we demonstrate that human-to-swine transmission has occurred frequently on a global scale over the past decades but that there is little persistence of human virus internal gene segments in swine.

Spillover of pH1N1 to swine in Cameroon: an investigation of risk factors

BACKGROUND

The 2009 pH1N1 influenza pandemic resulted in at least 18,500 deaths worldwide. While pH1N1 is now considered to be in a post-pandemic stage in humans it has nevertheless spilled back into swine in at least 20 countries. Understanding the factors that increase the risk of spillover events between swine and humans is essential to predicting and preventing future outbreaks. We assessed risk factors that may have led to spillover of pH1N1 from humans to swine in Cameroon, Central Africa. We sampled swine, domestic poultry and wild birds for influenza A virus at twelve sites in Cameroon from December 2009 while the pandemic was ongoing, to August 2012. At the same time we conducted point-count surveys to assess the abundance of domestic livestock and wild birds and assess interspecific contact rates. Random forest models were used to assess which variables were the best predictors of influenza in swine.

RESULTS

We found swine with either active pH1N1 infections or positive for influenza A at four of our 12 sites. Only one swine tested positive by competitive ELISA in 2011-2012. To date we have found pH1N1 only in the North and Extreme North regions of Cameroon (regions in Cameroon are administrative units similar to provinces), though half of our sites are in the Central and Western regions. Swine husbandry practices differ between the North and Extreme North regions where it is common practice in to let swine roam freely, and the Central and Western regions where swine are typically confined to pens. Random forest analyses revealed that the three best predictors of the presence of pH1N1 in swine were contact rates between free-ranging swine and domestic ducks, contact rates between free-ranging swine and wild Columbiformes, and contact rates between humans and ducks. Sites in which swine were allowed to range freely had closer contact with other species than did sites in which swine were kept penned.

CONCLUSIONS

Results suggest that the practice of allowing swine to roam freely is a significant risk factor for spillover of influenza from humans into swine populations.

Detection and isolation of 2009 pandemic influenza A/H1N1 virus in commercial piggery, Lagos Nigeria

WHO declared pandemic of A/H1N1 influenza in 2009 following global spread of the newly emerged strain of the virus from swine. Presently there is a dearth of data on the ecology of pandemic influenza H1N1 required for planning of intervention measures in sub Saharan Africa. Herein we report isolation of 2009 pandemic influenza A/H1N1 in an intensive mega piggery farms operation in South West Nigeria. Sentinel surveillance was carried out in a cohort of intensively reared pigs over a period of two years. Nasal swab specimens were collected at monthly interval from observed clinical cases of influenza like illness in pigs and pig handlers. Samples were analyzed by real time RT-PCR and isolation in chicken embryonated eggs. A total of 227 clinical cases of influenza like illness were observed among pigs out of which 31 (13.7%) were positive for influenza A matrix gene by real time RT-PCR. Virus isolation yielded 29 (12%) isolates out of which 18 (18%) were identified as influenza A/H1N1 by Heamaglutination Inhibition test using H1 antisera. RT-PCR positive samples were subtyped as 2009 pandemic A/H1N1 with subtype specific primers and probes. This is the first report of detection and isolation of pandemic influenza H1N1 from pigs in Nigeria. Continuous circulation of this virus in pigs may cause reassortments with seasonal influenza or mutations and substitutions in the gene that may result in the emergence of novel or pandemic influenza virus of economic and public health importance. Nigeria is considered a geographical hotspot of zoonotic diseases, which necessitate active surveillance and monitoring of emerging pandemic threats.

Swine influenza in sub-saharan Africa--current knowledge and emerging insights

Pigs have been associated with several episodes of influenza outbreaks in the past and are considered to play a significant role in the ecology of influenza virus. The recent 2009 pandemic influenza A/H1N1 virus originated from swine and not only did it cause widespread infection in humans, but was also transmitted back to swine in Asia, Europe and America. What may be the prevailing situation in Africa, particularly in sub-Saharan Africa, with respect to the circulation of classical swine or pandemic influenza? The ecology of influenza viruses, as well as the epidemiology of human or animal influenza, is poorly understood in the region. In particular, little is known about swine influenza in Africa despite the relevance of this production in the continent and the widespread pig husbandry operations in urban and rural areas. In this review, the gap in the knowledge of classical and pandemic swine influenza is attributed to negligence of disease surveillance, as well as to the economic and public health impact that the disease may cause in sub-Saharan Africa. However, emerging serological and virological evidence of swine influenza virus in some countries in the region underscores the importance of integrated surveillance to better understand the circulation and epidemiology of swine influenza, a disease of global economic and public health importance.

Influenza A(H1N1)pdm09 virus in pigs, Réunion Island

During 2009, pandemic influenza A(H1N1)pdm09 virus affected humans on Réunion Island. Since then, the virus has sustained circulation among local swine herds, raising concerns about the potential for genetic evolution of the virus and possible retransmission back to humans of variants with increased virulence. Continuous surveillance of A(H1N1)pdm09 infection in pigs is recommended.

Identification and analysis of the first 2009 pandemic H1N1 influenza virus from U.S. feral swine

The first case of pandemic H1N1 influenza (pH1N1) virus in feral swine in the United States was identified in Texas through the United States Department of Agriculture (USDA) Wildlife Services' surveillance program. Two samples were identified as pandemic influenza by reverse transcriptase quantitative PCR (RT-qPCR). Full-genome Sanger sequencing of all eight influenza segments was performed. In addition, Illumina deep sequencing of the original diagnostic samples and their respective virus isolation cultures were performed to assess the feasibility of using an unbiased whole-genome linear target amplification method and multiple sample sequencing in a single Illumina GAIIx lane. Identical sequences were obtained using both techniques. Phylogenetic analysis indicated that all gene segments belonged to the pH1N1 (2009) lineage. In conclusion, we have identified the first pH1N1 isolate in feral swine in the United States and have demonstrated the use of an easy unbiased linear amplification method for deep sequencing of multiple samples.

Global transmission of influenza viruses from humans to swine

To determine the extent to which influenza viruses jump between human and swine hosts, we undertook a large-scale phylogenetic analysis of pandemic A/H1N1/09 (H1N1pdm09) influenza virus genome sequence data. From this, we identified at least 49 human-to-swine transmission events that occurred globally during 2009-2011, thereby highlighting the ability of the H1N1pdm09 virus to transmit repeatedly from humans to swine, even following adaptive evolution in humans. Similarly, we identified at least 23 separate introductions of human seasonal (non-pandemic) H1 and H3 influenza viruses into swine globally since 1990. Overall, these results reveal the frequency with which swine are exposed to human influenza viruses, indicate that humans make a substantial contribution to the genetic diversity of influenza viruses in swine, and emphasize the need to improve biosecurity measures at the human-swine interface, including influenza vaccination of swine workers.

Evolution of novel reassortant A/H3N2 influenza viruses in North American swine and humans, 2009-2011

Novel H3N2 influenza viruses (H3N2v) containing seven genome segments from swine lineage triple-reassortant H3N2 viruses and a 2009 pandemic H1N1 (H1N1pdm09) matrix protein segment (pM) were isolated from 12 humans in the United States between August and December 2011. To understand the evolution of these novel H3N2 viruses in swine and humans, we undertook a phylogenetic analysis of 674 M sequences and 388 HA and NA sequences from influenza viruses isolated from North American swine during 2009-2011, as well as HA, NA, and M sequences from eight H3N2v viruses isolated from humans. We identified 34 swine influenza viruses (termed rH3N2p) with the same combination of H3, N2, and pM segments as the H3N2v viruses isolated from humans. Notably, these rH3N2p viruses were generated in swine via reassortment events between H3N2 viruses and the pM segment approximately 4 to 10 times since 2009. The pM segment has also reassorted with multiple distinct lineages of H1 virus, especially H1δ viruses. Importantly, the N2 segment of all H3N2v viruses isolated from humans is derived from a genetically distinct N2 lineage that has circulated in swine since being acquired by reassortment with seasonal human H3N2 viruses in 2001-2002, rather than from the N2 that is associated with the 1998 H3N2 swine lineage. The identification of this N2 variant may have implications for influenza vaccine design and the potential pandemic threat of H3N2v to human age groups with differing levels of prior exposure and immunity.