Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution

Influenza viruses are remarkably adept at surviving in the human population over a long timescale. The human influenza A virus continues to thrive even among populations with widespread access to vaccines, and continues to be a major cause of morbidity and mortality. The virus mutates from year to year, making the existing vaccines ineffective on a regular basis, and requiring that new strains be chosen for a new vaccine. Less-frequent major changes, known as antigenic shift, create new strains against which the human population has little protective immunity, thereby causing worldwide pandemics. The most recent pandemics include the 1918 'Spanish' flu, one of the most deadly outbreaks in recorded history, which killed 30-50 million people worldwide, the 1957 'Asian' flu, and the 1968 'Hong Kong' flu. Motivated by the need for a better understanding of influenza evolution, we have developed flexible protocols that make it possible to apply large-scale sequencing techniques to the highly variable influenza genome. Here we report the results of sequencing 209 complete genomes of the human influenza A virus, encompassing a total of 2,821,103 nucleotides. In addition to increasing markedly the number of publicly available, complete influenza virus genomes, we have discovered several anomalies in these first 209 genomes that demonstrate the dynamic nature of influenza transmission and evolution. This new, large-scale sequencing effort promises to provide a more comprehensive picture of the evolution of influenza viruses and of their pattern of transmission through human and animal populations. All data from this project are being deposited, without delay, in public archives.

Characterization of a human H5N1 influenza A virus isolated in 2003

In 2003, H5N1 avian influenza virus infections were diagnosed in two Hong Kong residents who had visited the Fujian province in mainland China, affording us the opportunity to characterize one of the viral isolates, A/Hong Kong/213/03 (HK213; H5N1). In contrast to H5N1 viruses isolated from humans during the 1997 outbreak in Hong Kong, HK213 retained several features of aquatic bird viruses, including the lack of a deletion in the neuraminidase stalk and the absence of additional oligosaccharide chains at the globular head of the hemagglutinin molecule. It demonstrated weak pathogenicity in mice and ferrets but caused lethal infection in chickens. The original isolate failed to produce disease in ducks but became more pathogenic after five passages. Taken together, these findings portray the HK213 isolate as an aquatic avian influenza A virus without the molecular changes associated with the replication of H5N1 avian viruses in land-based poultry such as chickens. This case challenges the view that adaptation to land-based poultry is a prerequisite for the replication of aquatic avian influenza A viruses in humans.

Mutations in the NS1 protein of swine influenza virus impair anti-interferon activity and confer attenuation in pigs

It has been shown previously that the nonstructural protein NS1 of influenza virus is an alpha/beta interferon (IFN-alpha/beta) antagonist, both in vitro and in experimental animal model systems. However, evidence of this function in a natural host has not yet been obtained. Here we investigated the role of the NS1 protein in the virulence of a swine influenza virus (SIV) isolate in pigs by using reverse genetics. The virulent wild-type A/Swine/Texas/4199-2/98 (TX/98) virus and various mutants encoding carboxy-truncated NS1 proteins were rescued. Growth properties of TX/98 viruses with mutated NS1, induction of IFN in tissue culture, and virulence-attenuation in pigs were analyzed and compared to those of the recombinant wild-type TX/98 virus. Our results indicate that deletions in the NS1 protein decrease the ability of the TX/98 virus to prevent IFN-alpha/beta synthesis in pig cells. Moreover, all NS1 mutant viruses were attenuated in pigs, and this correlated with the amount of IFN-alpha/beta induced in vitro. These data suggest that the NS1 protein of SIV is a virulence factor. Due to their attenuation, NS1-mutated swine influenza viruses might have a great potential as live attenuated vaccine candidates against SIV infections of pigs.

Controlling avian flu at the source

Global agricultural authorities should harmonize with the public-health sector to ensure the exchange of flu virus samples, and establish a single international standard for vaccines, say Robert Webster and Diane Hulse.

Antibodies to human-related H3 influenza A virus in Baikal seals (Phoca sibirica) and ringed seals (Phoca hispida) in Russia

Antibodies to influenza A virus were detected using enzyme-linked immunosorbent assay (ELISA) in the sera from two of seven Baikal seals (Phoca sibrica) and from five of six ringed seals (Phoca hispida) in Russia. In a hemagglutination-inhibition test using H1-H15 reference influenza A viruses, ELISA-positive sera from one Baikal seal and four ringed seals reacted to A/Aichi/2/68 (H3N2) and A/Bangkok/1/79 (H3N2) strains. One ringed seal serum sample reacted to A/seal/Massachusetts/1/80 (H7N7). The present results suggested that human-related H3 viruses were prevalent in Baikal seals and ringed seals inhabiting the central Russian Arctic.

Infectious disease: Vietnam's war on flu

Having suffered heavily from avian influenza in 2004, Vietnam might now be brewing the next human flu pandemic. Yet, as Peter Aldhous discovers, local researchers don't have the resources to investigate the risk properly.

The H5N1 avian flu virus that swept through Asian poultry flocks last year and killed at least 20 people in Vietnam is now believed to be endemic in southeast Asia. The UN Food and Agriculture Organization and the World Bank have established a two-year Avian Influenza Emergency Recovery Project for Vietnam, investing in diagnostic labs and disease surveillance. But field workers in Vietnam say that more will need to be done if a pandemic is to be avoided.

Alert to a European epidemic

Funds must be forthcoming for an effective EU Centre for Disease Control.

Bird flu data languish in Chinese journals

Health authorities in the dark as warnings go untranslated

Multiple lineages of antigenically and genetically diverse influenza A virus co-circulate in the United States swine population

Before the isolation of H3N2 viruses in 1998, swine influenza in the United States was an endemic disease caused exclusively by classical-swine H1N1 viruses. In this study we determined the antigenic and phylogenetic composition of a selection of currently circulating strains and revealed that, in contrast to the situation pre-1998, the swine population in the United States is now a dynamic viral reservoir containing multiple viral lineages. H3N2 viruses still circulate and representatives of each of two previously identified phylogenetic groups were isolated. H1N1 and H1N2 viruses were also identified. In addition to the genotypic diversity present, there was also considerable antigenic diversity seen. At least three antigenic profiles of H1 viruses were noted and all of the recent H3N2 viruses reacted poorly, if at all, to the index A/swine/Texas/4199-2/98 H3N2 antiserum in hemagglutination inhibition assays. The influenza reservoir in the United States swine population has thus gone from a stable single viral lineage to one where genetically and antigenically heterogenic viruses co-circulate. The growing complexity of influenza at this animal-human interface and the presence of viruses with a seemingly high affinity for reassortment makes the United States swine population an increasingly important reservoir of viruses with human pandemic potential.

H5N1 influenza: a protean pandemic threat

Infection with avian influenza A virus of the H5N1 subtype (isolates A/HK/212/03 and A/HK/213/03) was fatal to one of two members of a family in southern China in 2003. This incident was preceded by lethal outbreaks of H5N1 influenza in waterfowl, which are the natural hosts of these viruses and, therefore, normally have asymptomatic infection. The hemagglutinin genes of the A/HK/212/03-like viruses isolated from humans and waterfowl share the lineage of the H5N1 viruses that caused the first known cases of human disease in Hong Kong in 1997, but their internal protein genes originated elsewhere. The hemagglutinin of the recent human isolates has undergone significant antigenic drift. Like the 1997 human H5N1 isolates, the 2003 human H5N1 isolates induced the overproduction of proinflammatory cytokines by primary human macrophages in vitro, whereas the precursor H5N1 viruses and other H5N1 reassortants isolated in 2001 did not. The acquisition by the viruses of characteristics that enhance virulence in humans and waterfowl and their potential for wider distribution by infected migrating birds are causes for renewed pandemic concern.

Transmission of H7N7 avian influenza A virus to human beings during a large outbreak in commercial poultry farms in the Netherlands

BACKGROUND

An outbreak of highly pathogenic avian influenza A virus subtype H7N7 started at the end of February, 2003, in commercial poultry farms in the Netherlands. Although the risk of transmission of these viruses to humans was initially thought to be low, an outbreak investigation was launched to assess the extent of transmission of influenza A virus subtype H7N7 from chickens to humans.

METHODS

All workers in poultry farms, poultry farmers, and their families were asked to report signs of conjunctivitis or influenza-like illness. People with complaints were tested for influenza virus type A subtype H7 (A/H7) infection and completed a health questionnaire about type of symptoms, duration of illness, and possible exposures to infected poultry.

FINDINGS

453 people had health complaints--349 reported conjunctivitis, 90 had influenza-like illness, and 67 had other complaints. We detected A/H7 in conjunctival samples from 78 (26.4%) people with conjunctivitis only, in five (9.4%) with influenza-like illness and conjunctivitis, in two (5.4%) with influenza-like illness only, and in four (6%) who reported other symptoms. Most positive samples had been collected within 5 days of symptom onset. A/H7 infection was confirmed in three contacts (of 83 tested), one of whom developed influenza-like illness. Six people had influenza A/H3N2 infection. After 19 people had been diagnosed with the infection, all workers received mandatory influenza virus vaccination and prophylactic treatment with oseltamivir. More than half (56%) of A/H7 infections reported here arose before the vaccination and treatment programme.

INTERPRETATION

We noted an unexpectedly high number of transmissions of avian influenza A virus subtype H7N7 to people directly involved in handling infected poultry, and we noted evidence for person-to-person transmission. Our data emphasise the importance of adequate surveillance, outbreak preparedness, and pandemic planning.

Building awareness of the avian flu outbreak and its symptoms

The current outbreak of avian influenza in South East Asia has resulted in a small number of human deaths. Avian flu can pass from birds to humans, although the number of humans infected is low. The fear is that the avian flu virus could mutate in a human who was also infected with a common flu virus, creating a new strain that could pass from human to human. Nurses, especially those working in travel health, should keep themselves informed of the latest developments.

The WHO Global Influenza Program and its Animal Influenza Network

The World Health Organization (WHO) Global Influenza Program makes annual recommendations on influenza vaccine formulation and related activities. This results in 230 million annual doses of vaccine produced for human use. The success of this program is based on the collection and genetic and antigenic analyses of influenza viruses collected by the WHO Global Influenza Surveillance Program. New programs focus on pandemic preparedness and include development and distribution of testing reagents for emerging or potentially emerging human influenza viruses. WHO Animal Influenza Network focuses on aspects of ecology and molecular biology of animal influenza viruses in the context of human health.

[Distribution and circulation of influenza viruses in nature]

All of the known subtypes of influenza A viruses are circulating in ducks, providing the reservoir for the emergence of influenza viruses in all other species including humans. Each of the pandemic influenza virus strains that emerged in 20th century is a reassortant generated in pig co-infected with avian viruses and the preceding human strains. None of the 15 HA and 9 NA subtypes can be ruled out as potential candidates for future pandemics since avian viruses of any subtype can contribute genes in the generation of reassortants in pigs. To expand surveillance for influenza viruses in migratory and domestic ducks and geese, chickens, quail, and pigs of the world and to be informed about what influenza viruses are dominant in the animal reservoirs, we have started 'Program of Excellence for the Control of Influenza'. One of the aims of the program is to establish a library of influenza virus strains and their genes, where influenza virus strains isolated from animal species in the surveillance are thoroughly characterized, stored, and provided for the use of diagnosis and vaccine preparation for the control of future pandemics.

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.

Animal influenza virus surveillance

Influenza surveillance studies in humans and animals performed for many years have provided a wealth of data on the ecology and evolution of influenza viruses and their public health related and economical impact. Here we provide a brief overview of some of the data from the past and give our view on how the continued and intensified animal influenza virus surveillance may aid in the early recognition and management of outbreaks in the future.

[Interspecies transmission of influenza A viruses and influenza pandemics]

Molecular and genetic data are summarized on the origin of influenza A virus pandemic variants. Conceptual modifications of the reassortment theory of the origin of pandemic strains are discussed in connection with the appearance of new H5 and H9 avian influenza viruses, which caused the respiratory infection in man and which are presently in the focus of attention as possible agents of future pandemic.

Comparison of the pathogenesis of two genetically different H3N2 influenza A viruses in pigs

In 1997 and 1998, H3N2 influenza A viruses emerged among pigs in North America. Genetic analyses of the H3N2 isolates demonstrated that they had distinctly different genotypes. The most commonly isolated viruses in the United States have a triple-reassortant genotype, with the hemagglutinin, neuraminidase, and PB1 polymerase genes being of human influenza virus origin, the nucleoprotein, matrix, and nonstructural genes being of classical swine influenza virus origin, and the PA and PB2 polymerase genes being of avian influenza virus origin. In contrast, a wholly human H3N2 virus was isolated from a single baby pig in Ontario, Canada, in 1997, but it did not spread within the swine population. Genetic differences between this wholly human virus and the triple-reassortant viruses may affect their replication efficiencies in pigs. In the present study we compared the pathogenicities and replication kinetics of the wholly human virus and a triple-reassortant virus in 7-week-old pigs that were infected intranasally with 2 x 10(3) to 2 x 10(6) 50% tissue culture infective doses of virus. Our results demonstrate that the wholly human virus replicated to significantly lower titers and that the onset of virus shedding was delayed compared to the replication titers and the time of onset of virus shedding in triple-reassortant viruses. In addition, infection with the triple-reassortant virus was associated with moderate to severe gross pathological and histological pulmonary lesions, while infection with the wholly human virus induced only mild pulmonary changes.

Pathology of human influenza A (H5N1) virus infection in cynomolgus macaques (Macaca fascicularis)

Infection with influenza A (H5N1) virus, which has not been associated with respiratory disease in humans previously, caused clinical signs of acute respiratory distress syndrome and multiple-organ dysfunction syndrome with high mortality in humans in Hong Kong in 1997. To study the pathogenesis of this disease, we infected four cynomolgus monkeys (Macaca fascicularis) with 2.5 x 104 median tissue culture infectious dose (TCID50) of influenza virus A/Hong Kong/156/97 (H5N1) and euthanatized them 4 or 7 days after infection. The main lesion was a necrotizing broncho-interstitial pneumonia (4/4) similar to those found in primary influenza virus pneumonia in humans, with desquamation of respiratory epithelium (4/4), intra-alveolar hemorrhage (4/4), hyaline membrane formation (2/4), and infiltration with neutrophils and macrophages (4/4). Lesions in other organs consisted of a suppurative tonsillitis (2/4) and necrosis in lymphoid organs (1/4), kidney (1/4), and liver (1/4). By immunohistochemistry, influenza virus antigen was limited to pulmonary tissue (4/4) and tonsils (2/4). Based on these results, we suggest that the cynomolgus monkey is a suitable animal model for studying the pathogenesis of human H5N1 virus infection and that multiple-organ dysfunction syndrome in this disease may be caused by diffuse alveolar damage from virus replication in the lungs alone.

Serological evidence of transmission of human influenza A and B viruses to Caspian seals (Phoca caspica)

Seroepidemiological surveillance of influenza in Caspian seals (Phoca caspica) was conducted. Antibodies to influenza A virus were detected in 54% (7/13), 57% (4/7), 40% (6/15) and 26% (11/42) of the serum samples collected in 1993, 1997, 1998 and 2000 by enzyme-linked immunosorbent assay (ELISA). In an hemagglutination-inhibition (HI) test using H1-H15 reference influenza A viruses as antigens, more than half of the examined ELISA-positive sera reacted with an H3N2 prototype strain A/Aichi/2/68. These sera were then examined by HI test with a series of naturally occurring antigenic variants of human H3N2 virus, and H3 viruses of swine, duck, and equine origin. The sera reacted strongly with the A/Bangkok/1/79 (H3N2) strain, which was prevalent in humans in 1979-1981. The present results indicate that human A/Bangkok/1/79-like virus was transmitted to Caspian seals probably in the early 1980s, and was circulated in the population. Antibodies to influenza B virus were detected by ELISA in 14% (1/7) and 10% (4/42) serum samples collected from Caspian seals in 1997 and 2000, respectively. Our findings indicate that seal might be a reservoir of both influenza A and B viruses originated from humans.

Seroepidemiological evidence of avian H4, H5, and H9 influenza A virus transmission to pigs in southeastern China

Pig serum samples collected in southeastern China were examined for antibodies to influenza A viruses. Since the hemagglutination inhibition (HI) test does not accurately detect antibodies to the hemagglutinins (HAs) of "avian" influenza viruses, we utilized the neutralization (NT) test to detect subtype-specific antibodies to the HA of avian viruses in pig sera. Neutralizing antibodies to H1, H3, H4, and H5 influenza viruses were detected in the serum samples collected in 1977-1982 and 1998, suggesting that pigs in China have been sporadically infected with avian H4 and H5 viruses in addition to swine and human H1 and H3 viruses. Antibodies to H9 virus, on the other hand, were found only in the sera collected in 1998, not in those collected in 1977-1982, correlating with the recent spread in poultry and subsequent isolation of H9N2 viruses from pigs and humans in 1998. The present results indicate that avian influenza viruses have been transmitted to pig populations in southeastern China.

Serologic evidence of H1 swine Influenza virus infection in swine farm residents and employees

We evaluated seropositivity to swine and human H1 influenza viruses in 74 swine farm owners, employees, their family members, and veterinarians in rural south-central Wisconsin, compared with 114 urban Milwaukee, Wisconsin, residents. The number of swine farm participants with positive serum hemagglutination-inhibition (HI) antibody titers > or = 40 to swine influenza viruses (17/74) was significantly higher (p<0.001) than the number of seropositive urban control samples (1/114). The geometric mean serum HI antibody titers to swine influenza viruses were also significantly higher (p<0.001) among the farm participants. Swine virus seropositivity was significantly (p<0.05) associated with being a farm owner or a farm family member, living on a farm, or entering the swine barn > or = 4 days/week. Because pigs can play a role in generating genetically novel influenza viruses, swine farmers may represent an important sentinel population to evaluate the emergence of new pandemic influenza viruses.

Retrospective analysis of serum and nasal mucus from cattle in Northern Ireland for evidence of infection with influenza A virus

Eighty-four pairs of acute and convalescent serum samples collected in 1998 and 1999 from 17 outbreaks of respiratory disease, milk drop syndrome or diarrhoea in cattle were tested by haemagglutination inhibition against human influenza viruses A/Eng/333/80 (HIN1) and A/Eng/427/88 (H3N2). Antibodies to these viruses were present in the convalescent sera of 56.5 per cent and 58.8 per cent cattle tested, respectively, with 56 per cent of the animals seroconverting to one or both viruses. Titres were typically higher to A/Eng/427/88 (H3N2). Further testing of a subset of 21 of these serum pairs against the predominant H1N1 and H3N2 human and porcine strains circulating when the samples were collected revealed that the highest reactivity, in terms of both the magnitude of the recorded titres and the number of positive sera, was to human H3N2 strains. The titres to human H1N1 strains and to both porcine subtypes were low or absent. Attempts to isolate influenza A virus from nasal mucus or swab samples from 142 cattle from 46 cases of respiratory disease and/or milk drop syndrome by passage in embryonated specific pathogen-free eggs were unsuccessful.

Isolation from turkey breeder hens of a reassortant H1N2 influenza virus with swine, human, and avian lineage genes

Type A influenza viruses can infect a wide range of birds and mammals, but influenza in a particular species is usually considered to be species specific. However, infection of turkeys with swine H1N1 viruses has been documented on several occasions. This report documents the isolation of an H1N2 influenza virus from a turkey breeder flock with a sudden drop in egg production. Sequence analysis of the virus showed that it was a complex reassortant virus with a mix of swine-, human-, and avian-origin influenza genes. A swine influenza virus with a similar gene complement was recently reported from pigs in Indiana. Isolation and identification of the virus required the use of nonconventional diagnostic procedures. The virus was isolated in embryonated chicken eggs by the yolk sac route of inoculation rather than by the typical chorioallantoic sac route. Interpretation of hemagglutination-inhibition test results required the use of turkey rather than chicken red blood cells, and identification of the neuraminidase subtype required the use of alternative reference sera in the neuraminidase-inhibition test. This report provides additional evidence that influenza viruses can cross species and cause a disease outbreak, and diagnosticians must be aware that the variability of influenza viruses can complicate the isolation and characterization of new isolates.