Phylogenetic analysis of H1N2 isolates of influenza A virus from pigs in the United States

Zooming in on the molecular characteristics of swine influenza virus circulating in Colombia before and after the H1N1pdm09 virus

Influenza is one of the most critical viral agents involved in the respiratory disease complex affecting swine production systems worldwide. Despite the absence of vaccination against swine influenza virus in Colombia, the serologic reactivity to classic H1N1 and H3N2 subtypes reported since 1971 indicates the virus has been circulating in the country's swine population for several decades. However, successful isolation and sequencing of field virus from pigs was nonexistent until 2008, when H1N1 classical influenza virus was identified. One year later, due to the emergence of the influenza A (H1N1) pdm09 virus, responsible for the first global flu pandemic of the 21st century, it was introduced in the country. Therefore, to understand the impact of the introduction of the H1N1pdm09 virus in Colombia on the complexity and dynamics of influenza viruses previously present in the swine population, we carried out a study aiming to characterize circulating viruses genetically and establish possible reassortment events that might have happened between endemic influenza viruses before and after the introduction of the pandemic virus. A phylogenetic analysis of ten swine influenza virus isolates from porcine samples obtained between 2008 and 2015 was conducted. As a result, a displacement of the classical swine influenza virus with the pdmH1N1 virus in the swine population was confirmed. Once established, the pandemic subtype exhibited phylogenetic segregation based on a geographic pattern in all the evaluated segments. The evidence presents reassortment events with classic viruses in one of the first H1N1pdm09 isolates. Thus, this study demonstrates complex competition dynamics and variations in Colombian swine viruses through Drift and Shift.

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

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

Prevalence, distribution and risk factors of farmer reported swine influenza infection in Guangdong Province, China

A cross-sectional study was undertaken to better understand the husbandry, management and biosecurity practices of pig farms in Guangdong Province (GD), China to identify risk factors for farmer reported swine influenza (SI) on their farms. Questionnaires were administered to 153 owners/managers of piggeries (average of 7 from each of the 21 prefectures in GD). Univariable and multivariable logistic regression analyses were used to identify risk factors for farmer reported SI in piggeries during the six months preceding the questionnaire administration. The ability of wild birds to enter piggeries (OR 2.50, 95% CI: 1.01-6.16), the presence of poultry on a pig-farm (OR 3.24, 95% CI: 1.52-6.94) and no biosecurity measures applied to workers before entry to the piggery (OR 2.65, 95% CI: 1.04-6.78) were found to increase the likelihood of SI being reported by farmers in a multivariable logistic regression model. The findings of this study highlight the importance of understanding the local pig industry and the practices adopted when developing control measures to reduce the risk of SI to pig farms.

Pregnancy outcome and clinical status of gilts following experimental infection by H1N2, H3N2 and H1N1pdm09 influenza A viruses during the last month of gestation

The present study was planned to study the effect of various subtypes of swine influenza virus (SIV) circulating among pigs (H1N2, H3N2 and emerging pandemic strain of H1N1 influenza A virus (H1N1pdm09) on the course of pregnancy in naïve gilts experimentally infected during the last month of pregnancy. In addition, the clinical course of infection, distribution of viruses in various tissues (blood, placenta, fetal lung), and selected immunological, reproductive and productive parameters were also investigated. All SIV-inoculated gilts became infected. No abortions, stillbirths, intrauterine deaths or mummified fetuses were observed. No clinical signs of influenza virus infection or other disorders were observed in piglets born from infected and control gilts. There was a significant decrease in the number and frequency of lymphocytes in gilts inoculated with all influenza viruses. In general, the concentrations of IL-6, IL-10 and TNF-α were significantly higher in SIV-inoculated gilts as than in control animals, while IL-4 and IFN-γ were not detected in plasma at any time post-inoculation in SIV- or mock-inoculated gilts. No evidence for transplacental transmission of SIV was found. Viremia was also not observed in any of the infected females. On the basis of recent results, we hypothesize that pregnancy failure observed during SIV infection under field conditions is probably related to high fever and pro-inflammatory cytokines rather than a direct effect of the virus on the placenta, embryo or fetus.

CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences

Complex informational spectrum analysis for protein sequences (CISAPS) and its web-based server are developed and presented. As recent studies show, only the use of the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including absolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case study in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server. These associations are probable to be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as zero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino acid indices where each one represents a different property to perform the analysis. This web-based server enables researchers with little knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.

The influence of experimental infection of gilts with swine H1N2 influenza A virus during the second month of gestation on the course of pregnancy, reproduction parameters and clinical status

Background

The course of swine influenza in pigs is reported to be similar to human influenza. Occasionally abortions and other reproduction disorders have been associated with influenza A virus (IAV) infection in pigs. Abortions may be a consequence of high fever, pro-inflammatory cytokines or transplacental transmission of the virus.

The role of IAV in the complications observed during pregnancy has been scanty and the true importance of this agent as a cause of reproductive problems in swine is not known. The aim was to determine the possible involvement of swine H1N2 IAV strain on reproductive disorders in pregnant gilts under experimental conditions.

Results

The gestation length was from 113 to 116 days, no abortion or any other reproduction disorders were noted. A PCR assay confirms the presence of IAV in the nasal swabs taken from inoculated gilts between 1 and 5 dpi. In the nasal swabs from control gilts and newborn piglets, no IAV genetic material was found. No viral RNA was detected in samples of blood taken from gilts and piglets, placentas, lungs and tracheas taken from piglets euthanized after delivery. The significant decrease in the number and percentage of lymphocytes without leukopenia was observed at 4 dpi in inoculated gilts. The percentage of granulocytes increased significantly at 4 dpi in inoculated pigs. The concentration of IL-6, IL-10 and TNF-α were higher in inoculated gilts, while IL-4 and IFN-γ were not detected in the serum of any of animals. The serum concentrations of C-reactive protein remained stable during study, while haptoglobin concentrations increased significantly after inoculation.

Conclusions

The results of the study indicate that infection of pregnant gilts with swine H1N2 IAV in the second month of pregnancy does not cause abortion and other reproduction disorders. No evidence for transplacental transmission of swine H1N2 IAV was found. However, due to subclinical course of influenza in the present experiment caution should be taken in extrapolating these results to the cases of acute influenza. The other limitation is IAV diversity. It cannot be excluded that other subtypes of IAV could be associated to reproduction failure in pigs.

Vaccine development for protecting swine against influenza virus

Influenza virus infects a wide variety of species including humans, pigs, horses, sea mammals and birds. Weight loss caused by influenza infection and/or co-infection with other infectious agents results in significant financial loss in swine herds. The emergence of pandemic H1N1 (A/CA/04/2009/H1N1) and H3N2 variant (H3N2v) viruses, which cause disease in both humans and livestock constitutes a concerning public health threat. Influenza virus contains eight single-stranded, negative-sense RNA genome segments. This genetic structure allows the virus to evolve rapidly by antigenic drift and shift. Antigen-specific antibodies induced by current vaccines provide limited cross protection to heterologous challenge. In pigs, this presents a major obstacle for vaccine development. Different strategies are under development to produce vaccines that provide better cross-protection for swine. Moreover, overriding interfering maternal antibodies is another goal for influenza vaccines in order to permit effective immunization of piglets at an early age. Herein, we present a review of influenza virus infection in swine, including a discussion of current vaccine approaches and techniques used for novel vaccine development.

Kinetics of lung lesion development and pro-inflammatory cytokine response in pigs with vaccine-associated enhanced respiratory disease induced by challenge with pandemic (2009) A/H1N1 influenza virus

The objective of this report was to characterize the enhanced clinical disease and lung lesions observed in pigs vaccinated with inactivated H1N2 swine δ-cluster influenza A virus and challenged with pandemic 2009 A/H1N1 human influenza virus. Eighty-four, 6-week-old, cross-bred pigs were randomly allocated into 3 groups of 28 pigs to represent vaccinated/challenged (V/C), non-vaccinated/challenged (NV/C), and non-vaccinated/non-challenged (NV/NC) control groups. Pigs were intratracheally inoculated with pH1N1 and euthanized at 1, 2, 5, and 21 days post inoculation (dpi). Macroscopically, V/C pigs demonstrated greater percentages of pneumonia compared to NV/C pigs. Histologically, V/C pigs demonstrated severe bronchointerstitial pneumonia with necrotizing bronchiolitis accompanied by interlobular and alveolar edema and hemorrhage at 1 and 2 dpi. The magnitude of peribronchiolar lymphocytic cuffing was greater in V/C pigs by 5 dpi. Microscopic lung lesion scores were significantly higher in the V/C pigs at 2 and 5 dpi compared to NV/C and NV/NC pigs. Elevated TNF-α, IL-1β, IL-6, and IL-8 were detected in bronchoalveolar lavage fluid at all time points in V/C pigs compared to NV/C pigs. These data suggest H1 inactivated vaccines followed by heterologous challenge resulted in potentiated clinical signs and enhanced pulmonary lesions and correlated with an elevated proinflammatory cytokine response in the lung. The lung alterations and host immune response are consistent with the vaccine-associated enhanced respiratory disease (VAERD) clinical outcome observed reproducibly in this swine model.

Contemporary epidemiology of North American lineage triple reassortant influenza A viruses in pigs

The 2009 pandemic H1N1 infection in humans has been one of the greatest concerns for public health in recent years. However, influenza in pigs is a zoonotic viral disease well-known to virologists for almost one century with the classical H1N1 subtype the only responsible agent for swine influenza in the United States for many decades. Swine influenza was first recognized clinically in pigs in the Midwestern U.S. in 1918 and since that time it has remained important to the swine industry throughout the world. Since 1988, however, the epidemiology of swine influenza changed dramatically. A number of emerging subtypes and genotypes have become established in the U.S. swine population. The ability of multiple influenza virus lineages to infect pigs is associated with the emergence of reassortant viruses with new genomic arrangements, and the introduction of the 2009 pandemic H1N1 from humans to swine represents a well-known example. The recent epidemiological data regarding the current state of influenza A virus subtypes circulating in the Canadian and American swine population is discussed in this review.

Characterization of influenza a outbreaks in Minnesota swine herds and measures taken to reduce the risk of zoonotic transmission

Influenza A virus infections commonly cause respiratory disease in swine and can be transmitted between people and pigs, with potentially novel strains introduced into herds and spilling back into the human population. The goals of this study were to characterize influenza infections in Minnesota pigs and assess biosecurity measures used by swine workers. Veterinarians submitting influenza-positive swine samples to the University of Minnesota Veterinary Diagnostic Laboratory between October 2007 and April 2009 were surveyed regarding disease-related information and biosecurity procedures at each farm. Influenza-positive samples were submitted year-round, peaking in spring and fall. H1N1 was the most commonly detected subtype (56%), followed by H3N2 (14%) and H1N2 (12%). Most positive submissions were associated with illness in growing pigs (median age 8.8 weeks, IQR 5-15). Median morbidity and mortality were 25% (IQR 10-48) and 2% (IQR 0.5-3.5), respectively. Vaccination of sows and growing pigs was conducted at 71% and 7.9% of the swine farms, respectively. Specialized footwear was reported as the most common form of protective equipment used by workers. Employee vaccination for seasonal influenza was 19%. The sow vaccination rate in this study is consistent with national data, although growing pig vaccination is lower than the national average. Seasonal and age trends identified here may provide diagnostic guidance when growing pigs experience respiratory disease. Inconsistent use of protective equipment and employee vaccination at swine farms indicates the need for further discussion and research of approaches to minimize interspecies influenza transmission on swine farms.

The role of swine in the generation of novel influenza viruses

The ecology of influenza A viruses is very complicated involving multiple host species and viral genes. Avian species have variable susceptibility to influenza A viruses with wild aquatic birds being the reservoir for this group of pathogens. Occasionally, influenza A viruses are transmitted to mammals from avian species, which can lead to the development of human pandemic strains by direct or indirect transmission to man. Because swine are also susceptible to infection with avian and human influenza viruses, genetic reassortment between these viruses and/or swine influenza viruses can occur. The potential to generate novel influenza viruses has resulted in swine being labelled 'mixing vessels'. The mixing vessel theory is one mechanism by which unique viruses can be transmitted from an avian reservoir to man. Although swine can generate novel influenza viruses capable of infecting man, at present, it is difficult to predict which viruses, if any, will cause a human pandemic. Clearly, the ecology of influenza A viruses is dynamic and can impact human health, companion animals, as well as the health of livestock and poultry for production of valuable protein commodities. For these reasons, influenza is, and will continue to be, a serious threat to the wellbeing of mankind.

Evidence of reassortment of pandemic H1N1 influenza virus in swine in Argentina: are we facing the expansion of potential epicenters of influenza emergence?

Please cite this paper as: Pereda et al. (2011) Evidence of reassortment of pandemic H1N1 influenza virus in swine in Argentina: are we facing the expansion of potential epicenters of influenza emergence? Influenza and Other Respiratory Viruses 5(6), 409–412.

In this report, we describe the occurrence of two novel swine influenza viruses (SIVs) in pigs in Argentina. These viruses are the result of two independent reassortment events between the H1N1 pandemic influenza virus (H1N1pdm) and human‐like SIVs, showing the constant evolution of influenza viruses at the human–swine interface and the potential health risk of H1N1pdm as it appears to be maintained in the swine population. It must be noted that because of the lack of information regarding the circulation of SIVs in South America, we cannot discard the possibility that ancestors of the H1N1pdm or other SIVs have been present in this part of the world. More importantly, these findings suggest an ever‐expanding geographic range of potential epicenters of influenza emergence with public health risks.

Enhanced pneumonia and disease in pigs vaccinated with an inactivated human-like (δ-cluster) H1N2 vaccine and challenged with pandemic 2009 H1N1 influenza virus

Influenza is an economically important respiratory disease affecting swine world-wide with potential zoonotic implications. Genetic reassortment and drift has resulted in genetically and antigenically distinct swine influenza viruses (SIVs). Consequently, prevention of SIV infection is challenging due to the increased rate of genetic change and a potential lack of cross-protection between vaccine strains and circulating novel isolates. This report describes a vaccine-heterologous challenge model in which pigs were administered an inactivated H1N2 vaccine with a human-like (δ-cluster) H1 six and three weeks before challenge with H1 homosubtypic, heterologous 2009 pandemic H1N1. At necropsy, macroscopic and microscopic pneumonia scores were significantly higher in the vaccinated and challenged (Vx/Ch) group compared to non-vaccinated and challenged (NVx/Ch) pigs. The Vx/Ch group also demonstrated enhanced clinical disease and a significantly elevated pro-inflammatory cytokine profile in bronchoalveolar lavage fluid compared to the NVx/Ch group. In contrast, viral shedding and replication were significantly higher in NVx/Ch pigs although all challenged pigs, including Vx/Ch pigs, were shedding virus in nasal secretions. Hemagglutination inhibition (HI) and serum neutralizing (SN) antibodies were detected to the priming antigen in the Vx/Ch pigs but no measurable cross-reacting HI or SN antibodies were detected to pandemic H1N1 (pH1N1). Overall, these results suggest that inactivated SIV vaccines may potentiate clinical signs, inflammation and pneumonia following challenge with divergent homosubtypic viruses that do not share cross-reacting HI or SN antibodies.

Molecular and genetic analysis of NS gene from high pathogenic strains of the avian influenza (H5N1) virus isolated in Kazakhstan

The high pathogenic strains of the avian influenza H5N1 virus isolated in Kazakhstan have NS of different genotypes. The influenza virus strains isolated in 2005 is of NS1E Qinghai genotype. A/swan/Mangystau/3/2006 strain is of NS2A genotype that is typical for Gs/Gd-like strains. The results of the analysis allow assuming that A/swan/Mangystau/3/2006 strain has been brought onto the territory of Kazakhstan from the European part of the continent along the Black Sea-Mediterranean flyway.

Effects of windowing and zero-padding on Complex Resonant Recognition Model for protein sequence analysis

Signal processing techniques such as Fourier Transform have widely been studied and successfully applied in many different areas. Techniques such as zero-padding and windowing have been developed and found very useful to improve the outcome of the signal processing methods. Resonant Recognition Model (RRM) and Complex Resonant Recognition Model (CRRM) that are based on the discrete Fourier Transform and widely used for the analysis of protein sequences do not consider such methods, which can however improve or alter the features extracted from the protein sequences. Therefore, in this paper, an extensive analysis was carried out to investigate into the influence of the zero-padding and windowing on the features extracted from the Complex Resonant Recognition Model. In order to present such effects, five different classes of influenza A virus Neuraminidase genes, which include H1N1, H1N2, H2N2, H3N2 and H5N1 genes, were used as a case study. For each of the Influenza A subtypes, two sets of Common Frequency Peaks (CFP) were extracted, one where windowing is applied and the other one where windowing is suppressed, for each signal length set for the analysis. In order to make all the signals (protein sequence) the same length, zero-padding was used. The signal lengths used in this study are set to 470, which is the maximum protein length, and also 512, 1024, 2048, 4096, 8192 and 16384 for further analysis. The results suggest that the windowing and zero-padding have key impact on CFP extracted from the Influenza A subtypes as the best match with CFP extracted from influenza A subtypes using CRRM is when the signal length of 4096 and windowing were both applied. Therefore, the outcome of this study should be taken into consideration for more accurate and reliable analysis of the protein sequences.

Active reassortment of H9 influenza viruses between wild birds and live-poultry markets in Korea

Surveillance of H9 avian influenza viruses in Korean live-poultry markets from September 2004 through October 2007 was carried out to investigate active reassortment between wild migratory birds and domestic poultry in Korea. Antigenic and phylogenetic analyses showed that most of the isolates belong to the previous Korean H9N2-like lineage and differ from the southeastern Chinese strains. Interestingly, the Ck/Korea/LPM77/06 group (genotype B) and Dk/Korea/LPM248/07 group (genotype C) showed unique properties distinct from those of other Korean H9N2 strains. Although the HA genes of these two groups belong to Korean H9N2-like lineage, the PA genes closely resemble those of the Chinese Y280-like lineage. In addition, the PB2 genes of the Dk/Korea/LPM248/07 group were closely related to those isolated from migratory birds. Several other isolates also clustered within the H9N2 B genotype, an indication that there are at least two predominant H9N2 influenza genotypes in Korea. Another isolate, Dk/Korea/LPM71/06, was identified as an H9N1 subtype, the first ever discovered in Korean live-poultry markets. These findings reveal that reassortment of Korean H9 influenza viruses has occurred frequently in live-poultry markets and may have been mediated by introduction of genetic material from viruses circulating among migratory wild birds to domestic birds. Consequently, the new dominant H9N2 genotypes have become established in Korean live-poultry markets through continued reassortment.

Alterations in receptor-binding properties of swine influenza viruses of the H1 subtype after isolation in embryonated chicken eggs

Alterations of the receptor-binding properties of swine influenza A viruses (SIVs) during their isolation in embryonated chicken eggs have not been well studied. In this study, the receptor-binding properties of classical H1 SIVs isolated solely in eggs or Madin-Darby canine kidney (MDCK) cells were examined. Sequencing analysis revealed substitutions of D190V/N or D225G in the haemagglutinin (HA) proteins in egg isolates, whereas MDCK isolates retained HA genes identical to those of the original viruses present in the clinical samples. Egg isolates with substitution of either D190V/N or D225G had increased haemagglutinating activity for mouse and sheep erythrocytes, but reduced activity for rabbit erythrocytes. Additionally, egg isolates with D225G had increased haemagglutination activity for chicken erythrocytes. A direct binding assay using a sialyl glycopolymer that possessed either a 5-N-acetylneuraminic acid (Neu5Ac) alpha2,6galactose (Gal) or a Neu5Acalpha2,3Gal linkage revealed that the egg isolates used in this study showed higher binding activity to the Neu5Acalpha2,3Gal receptor than MDCK isolates. Increased binding activity of the egg isolates to the Neu5Acalpha2,3Gal receptor was also confirmed by haemagglutination assay with resialylated chicken erythrocytes by Galbeta1,3/4GlcNAcalpha2,3-sialyltransferase. These observations were reinforced by flow-cytometric and N-glycan analyses of the erythrocytes. The alpha2,3-linked sialic acids were expressed predominantly on the surface of mouse and sheep erythrocytes. Chicken erythrocytes expressed Neu5Acalpha2,3Gal more abundantly than Neu5Acalpha2,6Gal, and rabbit erythrocytes expressed both 5-N-glycolylneuraminic acid (Neu5Gc) alpha2,6Gal and Neu5Acalpha2,6Gal. Our results demonstrate clearly that classical H1 SIVs undergo alterations in receptor-binding activity associated with an amino acid substitution in the HA protein during isolation and propagation in embryonated chicken eggs.

Epidemiological update on swine influenza (H1N1) in pigs

The 2009 H1N1 pandemic has slowed down its spread after initial speed of transmission. The conventional swine influenza H1N1 virus (SIV) in pig populations worldwide needs to be differentiated from pandemic H1N1 influenza virus, however it is also essential to know about the exact role of pigs in the spread and mutations taking place in pig-to-pig transmission. The present paper reviews epidemiological features of classical SIV and its differentiation with pandemic influenza.

Swine influenza viruses a North American perspective

Influenza is a zoonotic viral disease that represents a health and economic threat to both humans and animals worldwide. Swine influenza (SI) was first recognized clinically in pigs in the Midwestern U.S., in 1918, coinciding with the human influenza pandemic known as the Spanish flu. Since that time SI has remained of importance to the swine industry throughout the world. In this review, the epidemiology of swine influenza virus (SIV) infection in North American pigs is described in detail. The first 80 years of SI remained relatively static, whereas the last decade has become dynamic with the establishment of many emerging subtypes. With the increasing number of novel subtypes and genetic variants, the control of SI has become increasingly difficult and innovative strategies to combat this economically important zoonotic disease are critical. Therefore, protective immune responses against influenza virus infections as well as new paradigms of vaccine development in pigs are discussed in the review. It is expected that the dynamic evolutionary changes of SIVs in North American pigs will continue, making currently available prophylactic approaches of limited use to control the spread and economic losses associated with this important swine pathogen.

Phylogenetic analysis of swine influenza viruses recently isolated in Korea

Several influenza A viral subtypes were isolated from pigs during a severe outbreak of respiratory disease in Korea during 2005 and 2006. They included a classical swine H1N1 subtype, two swine-human-avian triple-recombinant H1N2 subtypes, and a swine-human-avian triple-recombinant H3N2 subtype. In the current study, genetic characterization to determine the probable origin of these recent isolates was carried out for the first time. Phylogenetic analysis indicated that all the recent Korean isolates of H1N1, H1N2, and H3N2 influenza are closely related to viruses from the United States. Serologic and genetic analysis indicated that the Korean H1N2 viral subtypes were introduced directly from the United States, and did not arise from recombination between Korean H1N1 and H3N2. We suggest that the H1N1, H1N2, and H3N2 viral subtypes that were isolated from the Korean swine population originated in North America, and that these viruses are currently circulating in the Korean swine population.

Up to new tricks - a review of cross-species transmission of influenza A viruses

Influenza is a highly contagious disease that has burdened both humans and animals since ancient times. In humans, the most dramatic consequences of influenza are associated with periodically occurring pandemics. Pandemics require the emergence of an antigenically novel virus to which the majority of the population lacks protective immunity. Historically, influenza A viruses from animals have contributed to the generation of human pandemic viruses and they may do so again in the future. It is, therefore, critical to understand the epidemiological and molecular mechanisms that allow influenza A viruses to cross species barriers. This review summarizes the current knowledge of influenza ecology, and the viral factors that are thought to determine influenza A virus species specificity.

Evolutionary analyses of European H1N2 swine influenza A virus by placing timestamps on the multiple reassortment events

A novel H1N2 swine influenza A virus emerged in Europe since 1994. Previous phylogenetic analyses revealed that its genome segments were derived from H1N1 human virus, H3N2 human virus and avian-like H1N1/H3N2 swine virus, indicating the possibility of multiple reassortments events. However, dates of these reassortment events have not been investigated systematically. In this study, we used both global and local molecular clock concepts in a maximum likelihood framework to extrapolate the times of origins of the genome segments in European H1N2 swine viruses, and deduced that novel neuraminidase, hemagglutinin and other internal protein genes were introduced to the European H1N2 lineage at the 1970s, early 1980s and late 1980s, respectively through reassortments. Furthermore, in light of the evolutionary timescale reconstructed for the H1N2 viruses, we argue that further reassortments, in addition to those responsible for the introductions of novel genome segments, might have also occurred among the viruses prior to the outbreaks arose in United Kingdom at 1994. Our results confirm that the viral genes of various origins have stably maintained in swine population for many years before the multiple genetic reassortant was detected. Our evolutionary analyses also suggested that the HA and NA genes evolved in a significantly higher rate of synonymous substitutions after they were introduced from human to swine and established the European H1N2 swine lineage.

Efficacy of intranasal administration of a truncated NS1 modified live influenza virus vaccine in swine

In the U.S., despite available swine influenza virus (SIV) vaccines, multiple influenza subtypes as well as antigenic and genetic variants within subtypes continue to circulate in the swine population. One of the challenges to control and eliminate SIV is that the currently used inactivated influenza virus vaccines do not provide adequate cross-protection against multiple antigenic variants of SIV in the field. We previously generated a recombinant H3N2 swine influenza virus (SIV) based on the influenza A/SW/TX/4199-2/98 virus (TX98) containing an NS1 gene expressing a truncated NS1 protein of 126 amino acids, TX98-NS1Delta126 virus. This recombinant strain was demonstrated to be highly attenuated in swine and showed potential for use as a modified live-virus vaccine (MLV) after intratracheal application in pigs. However, this route of inoculation is not practical for vaccination in the field. In the present study, we first compared intramuscular and intranasal routes of application of the MLV, and found that the intranasal route was superior in priming the local (mucosal) immune response. Pigs were then vaccinated via the intranasal route and challenged with wild type homologous TX98 H3N2 virus, with a genetic and antigenic variant H3N2 SIV (influenza A/SW/CO/23619/99 virus, CO99) and a heterosubtypic H1N1 SIV (influenza A/SW/IA/00239/2004 virus, IA04). The intranasally vaccinated pigs were completely protected against homologous challenge. In addition, MLV vaccination provided nearly complete protection against the antigenic H3N2 variant CO99 virus. When challenged with the H1N1 IA04 virus, MLV vaccinated animals displayed reduced fever and virus titers despite minimal reduction in lung lesions. In vaccinated pigs, there was no serologic cross-reactivity by HI assays with the heterologous or heterosubtypic viruses. However, there appeared to be substantial cross-reactivity in antibodies at the mucosal level with the CO99 virus in MLV vaccinated pigs.

Failure of protection and enhanced pneumonia with a US H1N2 swine influenza virus in pigs vaccinated with an inactivated classical swine H1N1 vaccine

Two US swine influenza virus (SIV) isolates, A/Swine/Iowa/15/1930 H1N1 (IA30) and A/Swine/Minnesota/00194/2003 H1N2 (MN03), were evaluated in an in vivo vaccination and challenge model. Inactivated vaccines were prepared from each isolate and used to immunize conventional pigs, followed by challenge with homologous or heterologous virus. Both inactivated vaccines provided complete protection against homologous challenge. However, the IA30 vaccine failed to protect against the heterologous MN03 challenge. Three of the nine pigs in this group had substantially greater percentages of lung lesions, suggesting the vaccine potentiated the pneumonia. In contrast, priming with live IA30 virus provided protection from nasal shedding and virus replication in the lung in MN03 challenged pigs. These data indicate that divergent viruses that did not cross-react serologically did not provide complete cross-protection when used in inactivated vaccines against heterologous challenge and may have enhanced disease. In addition, live virus infection conferred protection against heterologous challenge.

Serologic surveillance of swine H1 and H3 and avian H5 and H9 influenza A virus infections in swine population in Korea

Influenza A is a respiratory disease common in the swine industry. Three subtypes, H1N1, H1N2 and H3N2 influenza A viruses, are currently co-circulating in swine populations in Korea. An outbreak of the highly pathogenic avian influenza H5N1 virus occurred in domestic bird farms in Korea during the winter season of 2003. Pigs can serve as hosts for avian influenza viruses, enabling passage of the virus to other mammals and recombination of mammalian and avian influenza viruses, which are more readily transmissible to humans. This study reports the current seroprevalence of swine H1 and H3 influenza in swine populations in Korea by hemagglutination inhibition (HI) assay. We also investigated whether avian H5 and H9 influenza transmission occurred in pigs from Korea using both the HI and neutralization (NT) tests. 51.2% (380/742) of serum samples tested were positive against the swine H1 virus and 43.7% (324/742) were positive against the swine H3 virus by HI assay. The incidence of seropositivity against both the swine H1 virus and the swine H3 virus was 25.3% (188/742). On the other hand, none of the samples tested showed seropositivity against either the avian H5 virus or the avian H9 virus by the HI and NT tests. Therefore, we report the high current seroprevalence and co-infectivity of swine H1 and H3 influenza viruses in swine populations and the lack of seroepidemiological evidence of avian H5 and H9 influenza transmission to Korean pigs.

Serological profiles after consecutive experimental infections of pigs with European H1N1, H3N2, and H1N2 swine influenza viruses

Swine influenza viruses (SIVs) of H1N1, H3N2, and H1N2 subtypes, with antigenically different hemagglutinins, are currently cocirculating in pigs in Europe. This study aimed to determine whether the hemagglutination inhibition (HI) test, which is the primary serological test for SIV, is sufficiently specific to discriminate between infections with the three subtypes. In experiment 1, pigs were consecutively inoculated with European H1N1, H3N2, and H1N2 SIVs by the intranasal route, or with the respective subtypes only. In a second experiment, a commercial, inactivated H1N1- and H3N2- based SIV vaccine was administered once to pigs previously infected with one to three SIV subtypes or to influenza-naive pigs. Sequential serum samples were examined in HI and virus-neutralizing (VN) tests to the three strains used for pig inoculations. Of the 160 sera collected after infection with one or two SIV subtypes, only 8 showed cross-reactive antibodies to the remaining subtype(s) in the HI test, and 11 in the VN test. Consecutive inoculations with H1N1 and H1N2 or vice versa were followed by a significant rise in preexisting antibody titers to the first subtype after the second inoculation. When dually infection-immune pigs were inoculated with the third, remaining SIV subtype, nasal virus excretion was undetectable or reduced and the serological response was absent to moderate. A single vaccination of infection-immune pigs resulted in a dramatic rise in HI and VN antibody titers to any of the previously encountered subtypes, whereas SIV-naive pigs barely seroconverted. Most important, pigs previously infected with H1N1 but not with H1N2 developed crossreactive antibodies to H1N2 after the vaccination. In conclusion, the HI test remains adequate for the differential diagnosis of infections with H1N1, H3N2, and H1N2 in European swine populations if it is properly used and if the SIV vaccination status is taken into account.

Vaccination of pigs against swine influenza viruses by using an NS1-truncated modified live-virus vaccine

Swine influenza viruses (SIV) naturally infect pigs and can be transmitted to humans. In the pig, genetic reassortment to create novel influenza subtypes by mixing avian, human, and swine influenza viruses is possible. An SIV vaccine inducing cross-protective immunity between different subtypes and strains circulating in pigs is highly desirable. Previously, we have shown that an H3N2 SIV (A/swine/Texas/4199-2/98 [TX98]) containing a deleted NS1 gene expressing a truncated NS1 protein of 126 amino acids, NS1black triangle126, was attenuated in swine. In this study, 4-week-old pigs were vaccinated with the TX98 NS1black triangle126 modified live virus (MLV). Ten days after boosting, pigs were challenged with wild-type homologous H3N2 or heterosubtypic H1N1 SIV and sacrificed 5 days later. The MLV was highly attenuated and completely protected against challenge with the homologous virus. Vaccinated pigs challenged with the heterosubtypic H1N1 virus demonstrated macroscopic lung lesions similar to those of the unvaccinated H1N1 control pigs. Remarkably, vaccinated pigs challenged with the H1N1 SIV had significantly lower microscopic lung lesions and less virus shedding from the respiratory tract than did unvaccinated, H1N1-challenged pigs. All vaccinated pigs developed significant levels of hemagglutination inhibition and enzyme-linked immunosorbent assay titers in serum and mucosal immunoglobulin A antibodies against H3N2 SIV antigens. Vaccinated pigs were seronegative for NS1, indicating the potential use of the TX98 NS1black triangle126 MLV as a vaccine to differentiate infected from vaccinated animals.

Isolation and characterization of novel H3N1 swine influenza viruses from pigs with respiratory diseases in Korea

Pigs can play an important role in the genetic reassortment of influenza viruses and as a reservoir for another lineage of influenza viruses that have the ability to reassort and be transmitted between species. In March and April 2006, novel H3N1 influenza A viruses were isolated from pigs with respiratory diseases at two different commercial swine farms in Korea. Genetic and phylogenetic analyses of the sequences of all eight viral RNA segments showed that the novel H3N1 swine influenza viruses were reassortants that acquired the hemagglutinin gene from an H3 human-like virus and other genes from swine influenza viruses that are currently circulating in Korea. Serologic and virologic tests in the infected farms suggested that pig-to-pig and farm-to-farm transmissions occurred. Clinical signs in pigs and experimentally infected mice suggest the potential to transmit the virus between swine and other mammalian hosts. To our knowledge, this is the first report of the isolation of the swine H3N1 subtype from domestic pigs under field conditions in Korea. Further surveillance will be needed to determine whether this novel subtype will continue to circulate in the swine population.

Evaluation of hemagglutinin subtype 1 swine influenza viruses from the United States

Swine influenza viruses (SIV) of the hemagglutinin subtype 1 (H1) isolated from the United States (U.S.) have not been well-characterized in the natural host. An increase in the rate of mutation and reassortment has occurred in SIV isolates from the U.S. since 1998, including viruses belonging to the H1 subtype. Two independent animal studies were done to evaluate and compare the pathogenesis of 10 SIV isolates dating from 1930 to currently circulating isolates. In addition, the hemagglutinin and neuraminidase genes of each isolate were sequenced for genetic comparison, and serological cross-reactivity was evaluated using all sera and virus combinations in hemagglutination inhibition and serum neutralization assays. Statistically significant differences in percentage of pneumonia and virus titers in the lung were detected between isolates, with modern isolates tending to produce more severe disease, have more virus shedding and higher viral titers. However, nasal shedding and virus titers in the lung were not always correlated with one another or lung lesions. Serologically, the classic historical H1N1 viruses tended to have better cross-reaction between historical sera and antigens, with moderate to good cross-reactivity with modern viral antigens. However, the modern sera were less reactive with historical viruses. Modern viruses tended to have less consistent cross-reactivity within the modern group. Overall, H1 isolates collected over the last 75 years from the U.S. pig population exhibit considerable variability in pathogenicity. There appears to be an increase in genetic and antigenic diversity coincident with the emergence of the swine triple reassortant H3N2 in 1998.

Isolation and genetic characterization of new reassortant H3N1 swine influenza virus from pigs in the midwestern United States

Since the introduction of H3N2 swine influenza viruses (SIVs) into U.S. swine in 1998, H1N2 and H1N1 reassortant viruses have emerged from reassortment between classical H1N1 and H3N2 viruses. In 2004, a new reassortant H3N1 virus (A/Swine/Minnesota/00395/2004) was identified from coughing pigs. Phylogenetic analyses revealed a hemagglutinin segment similar to those of contemporary cluster III H3N2 SIVs and a neuraminidase sequence of contemporary H1N1 origin. The internal genes were of swine, human, and avian influenza virus origin, similar to those of contemporary U.S. cluster III H3N2 SIVs. The recovery of H3N1 is further evidence of reassortment among SIVs and justifies continuous surveillance.

Identification of human H1N2 and human-swine reassortant H1N2 and H1N1 influenza A viruses among pigs in Ontario, Canada (2003 to 2005)

Since 2003, three novel genotypes of H1 influenza viruses have been recovered from Canadian pigs, including a wholly human H1N2 virus and human-swine reassortants. These isolates demonstrate that human-lineage H1N2 viruses are infectious for pigs and that viruses with a human PB1/swine PA/swine PB2 polymerase complex can replicate in pigs.

The immune response and maternal antibody interference to a heterologous H1N1 swine influenza virus infection following vaccination

This study investigated the efficacy of a bivalent swine influenza virus (SIV) vaccine in piglets challenged with a heterologous H1N1 SIV isolate. The ability of maternally derived antibodies (MDA) to provide protection against a heterologous challenge and the impact MDA have on vaccine efficacy were also evaluated. Forty-eight MDA(+) pigs and 48 MDA(-) pigs were assigned to 8 different groups. Vaccinated pigs received two doses of a bivalent SIV vaccine at 3 and 5 weeks of age. The infected pigs were challenged at 7 weeks of age with an H1N1 SIV strain heterologous to the H1N1 vaccine strain. Clinical signs, rectal temperature, macroscopic and microscopic lesions, virus excretion, serum and local antibody responses, and influenza-specific T-cell responses were measured. The bivalent SIV vaccine induced a high serum hemagglutination-inhibition (HI) antibody titer against the vaccine virus, but antibodies cross-reacted at a lower level to the challenge virus. This study determined that low serum HI antibodies to a challenge virus induced by vaccination with a heterologous virus provided protection demonstrated by clinical protection and reduced pneumonia and viral excretion. The vaccine was able to prime the local SIV-specific antibody response in the lower respiratory tract as well as inducing a systemic SIV-specific memory T-cell response. MDA alone were capable of suppressing fever subsequent to infection, but other parameters showed reduced protection against infection compared to vaccination. The presence of MDA at vaccination negatively impacted vaccine efficacy as fever and clinical signs were prolonged, and unexpectedly, SIV-induced pneumonia was increased compared to pigs vaccinated in the absence of MDA. MDA also suppressed the serum antibody response and the induction of SIV-specific memory T-cells following vaccination. The results of this study question the effectiveness of the current practice of generating increased MDA levels through sow vaccination in protecting piglets against disease.

Evaluation of a recombinant human adenovirus-5 vaccine administered via needle-free device and intramuscular injection for vaccination of pigs against swine influenza virus

OBJECTIVE

To evaluate the safety and efficacy of a human adenovirus-5 vaccine for protecting weaned pigs against swine influenza virus subtype H3N2 infection when administered via 2 injection methods.

ANIMALS

76 pigs.

PROCEDURE

6 groups of weaned pigs received a 10-fold serial dilution of recombinant adenovirus expressing H3 hemagglutinin and a constant amount of recombinant adenovirus expressing nucleoprotein, either via a needle-free injection device or by traditional IM injection. In each group of 10 pigs, 1 served as a nonvaccinated contact pig to monitor whether there was spread of vaccinial virus from pig to pig. Vaccinated pigs and nonvaccinated controls were challenged or sham-inoculated 5 weeks later. After challenge, pigs were observed for clinical signs and nasal secretions were tested for virus. On day 5 after challenge, pigs were euthanatized; lungs were examined for gross lesions, and bronchoalveolar lavage specimens were tested for virus replication.

RESULTS

A hemagglutination inhibition (HI) antibody response was elicited in a dose-dependent manner. Traditional IM administered vaccination induced consistently higher HI antibody responses than vaccination via needle-free injection, but the differences were not significant. Likewise, traditional IM administration was superior at reducing nasal virus shedding except at the highest dose, at which both methods blocked virus replication. The severity of lung lesions was reduced in a dose-dependent manner by both vaccination methods. Sentinel pigs did not seroconvert.

CONCLUSIONS AND CLINICAL RELEVANCE

The human adenovirus-5 vaccine at high doses prevented nasal virus shedding after challenge exposure with both methods of administration. The replication-defective vaccine virus was not transmitted to sentinel pigs.

Are swine workers in the United States at increased risk of infection with zoonotic influenza virus?

BACKGROUND

Pandemic influenza strains originate in nonhuman species. Pigs have an important role in interspecies transmission of the virus. We examined multiple swine-exposed human populations in the nation's number 1 swine-producing state for evidence of previous swine influenza virus infection.

METHODS

We performed controlled, cross-sectional seroprevalence studies among 111 farmers, 97 meat processing workers, 65 veterinarians, and 79 control subjects using serum samples collected during the period of 2002-2004. Serum samples were tested using a hemagglutination inhibition assay against the following 6 influenza A virus isolates collected recently from pigs and humans: A/Swine/WI/238/97 (H1N1), A/Swine/WI/R33F/01 (H1N2), A/Swine/Minnesota/593/99 (H3N2), A/New Caledonia/20/99 (H1N1), A/Panama/2007/99 (H3N2), and A/Nanchang/933/95 (H3N2).

RESULTS

Using multivariable proportional odds modeling, all 3 exposed study groups demonstrated markedly elevated titers against the H1N1 and H1N2 swine influenza virus isolates, compared with control subjects. Farmers had the strongest indication of exposure to swine H1N1 virus infection (odds ratio [OR], 35.3; 95% confidence interval [CI], 7.7-161.8), followed by veterinarians (OR, 17.8; 95% CI, 3.8-82.7), and meat processing workers (OR, 6.5; 95% CI, 1.4-29.5). Similarly, farmers had the highest odds for exposure to swine H1N2 virus (OR, 13.8; 95% CI, 5.4-35.4), followed by veterinarians (OR, 9.5; 95% CI, 3.6-24.6) and meat processing workers (OR, 2.7; 95% CI, 1.1-6.7).

CONCLUSIONS

Occupational exposure to pigs greatly increases workers' risk of swine influenza virus infection. Swine workers should be included in pandemic surveillance and in antiviral and immunization strategies.

H3N2 influenza virus transmission from swine to turkeys, United States

Swinelike H3N2 influenza viruses were isolated from two geographically distinct turkey farms in the United States.

In 1998, a novel H3N2 reassortant virus emerged in the United States swine population. We report the interspecies transmission of this virus to turkeys in two geographically distant farms in the United States in 2003. This event is of concern, considering the reassortment capacity of this virus and the susceptibility of turkey to infection by avian influenza viruses. Two H3N2 isolates, A/turkey/NC/16108/03 and A/turkey/MN/764/03, had 98.0% to 99.9% nucleotide sequence identity to each other in all eight gene segments. All protein components of the turkey isolates had 97% to 98% sequence identity to swine H3N2 viruses, thus demonstrating interspecies transmission from pigs to turkeys. The turkey isolates were better adapted to avian hosts than were their closest swine counterparts, which suggests that the viruses had already begun to evolve in the new host. The isolation of swine-like H3N2 influenza viruses from turkeys raises new concerns for the generation of novel viruses that could affect humans.

Avian influenza viruses in Korean live poultry markets and their pathogenic potential

We surveyed live-poultry markets in Korea in 2003 and isolated 9 H9N2, 6 H3N2, and 1 H6N1 influenza viruses. Antigenic and phylogenetic analyses showed that all 9 H9N2 isolates were of A/Chicken/Korea/25232-96006/96-like lineage (which caused disease in chickens in Korea in 1996) but were different from H9N2 viruses of southeastern China. They had at least 4 genotypes and replicated in chickens but not in mice. The H3N2 and H6N1 viruses were new to Korea and were probably reassortants of avian influenza viruses from southeastern China and recent Korean H9N2 viruses. All 8 segments of the H3N2 viruses formed a single phylogenetic cluster with 99.1 to 100% homology. The H3N2 viruses replicated in chickens and mice without preadaptation, but the H6N1 virus did not. Our results show an increasingly diverse pool of avian influenza viruses in Korea that are potential pandemic influenza agents.

Continuing evolution of H9N2 influenza viruses in Southeastern China

H9N2 influenza viruses are panzootic in domestic poultry in Eurasia and since 1999 have caused transient infections in humans and pigs. To investigate the zoonotic potential of H9N2 viruses, we studied the evolution of the viruses in live-poultry markets in Hong Kong in 2003. H9N2 was the most prevalent influenza virus subtype in the live-poultry markets between 2001 and 2003. Antigenic and phylogenetic analysis of hemagglutinin (HA) showed that all of the 19 isolates found except one belonged to the lineage represented by A/Duck/Hong Kong/Y280/97 (H9N2). The exception was A/Guinea fowl/NT184/03 (H9N2), whose HA is most closely related to that of the human isolate A/Guangzhou/333/99 (H9N2), a virus belonging to the A/Chicken/Beijing/1/94-like (H9N2) lineage. At least six different genotypes were recognized. The majority of the viruses had nonstructural (and HA) genes derived from the A/Duck/Hong Kong/Y280/97-like virus lineage but had other genes of mixed avian virus origin, including genes similar to those of H5N1 viruses isolated in 2001. Viruses of all six genotypes of H9N2 found were able to replicate in chickens and mice without adaptation. The infected chickens showed no signs of disease, but representatives of two viral genotypes were lethal to mice. Three genotypes of virus replicated in the respiratory tracts of swine, which shed virus for at least 5 days. These results show an increasing genetic and biologic diversity of H9N2 viruses in Hong Kong and support their potential role as pandemic influenza agents.

Characterization of avian H3N3 and H1N1 influenza A viruses isolated from pigs in Canada

H3N3 and H1N1 influenza A viruses were isolated from Canadian pigs in 2001 and 2002. These viruses are phylogenetically related to waterfowl viruses and antigenically distinct from reference swine influenza viruses. The isolation of these viruses reemphasizes the potential for interspecies transmission of influenza viruses from waterfowl to pigs in North America.

Influenza A viruses in feral Canadian ducks: extensive reassortment in nature

The current dogma of influenza accepts that feral aquatic birds are the reservoir for influenza A viruses. Although the genomic information of human influenza A viruses is increasing, little of this type of data is available for viruses circulating in feral waterfowl. This study presents the genetic characterization of 35 viruses isolated from wild Canadian ducks from 1983 to 2000, as the first attempt at a comprehensive genotypic analysis of influenza viruses isolated from feral ducks. This study demonstrates that influenza virus genes circulating in Canadian ducks have achieved evolutionary stasis. The majority of these duck virus genes are clustered in distinct North American clades; however, some H6 and H9 genes are clustered with those from Eurasian viruses. Genes appeared to reassort in a random fashion. None of the genotypes identified remained present throughout all of the years examined and most PA and PB2 genes that crossed over into swine were clustered in one phylogenetic grouping. Additionally, matrix genes were identified that branch very early in the evolutionary tree. These findings demonstrate the diversity of the influenza virus gene pool in Canadian ducks, and suggest that genes which cluster in specific phylogenetic groupings in the PB2 and PA genes can be used for markers of viruses with the potential for crossing the species barrier. A more comprehensive study of this important reservoir is needed to provide further insight into the genomic composition of viruses that crossover the species barrier, which would be a useful component to pandemic planning.

Pathogenic and antigenic properties of phylogenetically distinct reassortant H3N2 swine influenza viruses cocirculating in the United States

Swine influenza is an acute respiratory disease caused by type A influenza viruses. Before 1998, swine influenza virus isolates in the United States were mainly of the classical H1N1 lineage. Since then, phylogenetically distinct reassortant H3N2 viruses have been identified as respiratory pathogens in pigs on U.S. farms. The H3N2 viruses presently circulating in the U.S. swine population are triple reassortants containing avian-like (PA and PB2), swine-like (M, NP, and NS), and human-like (HA, NA, and PB1) gene segments. Recent sequence data show that the triple reassortants have acquired at least three distinct H3 molecules from human influenza viruses and thus form three distinct phylogenetic clusters (I to III). In this study we analyzed the antigenic and pathogenic properties of viruses belonging to each of these clusters. Hemagglutination inhibition and neutralization assays that used hyperimmune sera obtained from caesarian-derived, colostrum-deprived pigs revealed that H3N2 cluster I and cluster III viruses share common epitopes, whereas a cluster II virus showed only limited cross-reactivity. H3N2 viruses from each of the three clusters were able to induce clinical signs of disease and associated lesions upon intratracheal inoculation into seronegative pigs. There were, however, differences in the severity of lesions between individual strains even within one antigenic cluster. A correlation between the severity of disease and pig age was observed. These data highlight the increased diversity of swine influenza viruses in the United States and would indicate that surveillance should be intensified to determine the most suitable vaccine components.