Influenza Virus Sequences Research Articles

The Recent Establishment of North American H10 Lineage Influenza Viruses in Australian Wild Waterfowl and the Evolution of Australian Avian Influenza Viruses

Influenza A H10N7 virus with a hemagglutinin gene of North American origin was detected in Australian chickens and poultry abattoir workers in New South Wales, Australia, in 2010 and in chickens in Queensland, Australia, on a mixed chicken and domestic duck farm in 2012. We investigated their genomic origins by sequencing full and partial genomes of H10 viruses isolated from wild aquatic birds and poultry in Australia and analyzed them with all available avian influenza virus sequences from Oceania and representative viruses from North America and Eurasia. Our analysis showed that the H10N7 viruses isolated from poultry were similar to those that have been circulating since 2009 in Australian aquatic birds and that their initial transmission into Australia occurred during 2007 and 2008. The H10 viruses that appear to have developed endemicity in Australian wild aquatic birds were derived from several viruses circulating in waterfowl along various flyways. Their hemagglutinin gene was derived from aquatic birds in the western states of the United States, whereas the neuraminidase was closely related to that from viruses previously detected in waterfowl in Japan. The remaining genes were derived from Eurasian avian influenza virus lineages. Our analysis of virological data spanning 40 years in Oceania indicates that the long-term evolutionary dynamics of avian influenza viruses in Australia may be determined by climatic changes. The introduction and long-term persistence of avian influenza virus lineages were observed during periods with increased rainfall, whereas bottlenecks and extinction were observed during phases of widespread decreases in rainfall. These results extend our understanding of factors affecting the dynamics of avian influenza and provide important considerations for surveillance and disease control strategies.

Genome Sequence of a Novel H10N9 Avian Influenza Virus Isolated from Chickens in a Live Poultry Market in Eastern China.

An H10N9 avian influenza virus (AIV) strain, A/Chicken/Jiangsu/RD5/2013, was isolated in China. The hemagglutinin (HA) and neuraminidase (NA) genes in this strain originated from H10N1 and H7N9 AIVs, respectively, and the other genes derived from H7N3 AIVs. Sequence analysis implies that the H10N9 AIV may be an NA gene donor for the human H7N9 influenza viruses.

Complete Genome Sequence of a New H9N2 Avian Influenza Virus Isolated in China.

The complete genomic sequence of a new H9N2 avian influenza virus (AIV), isolated in northwestern China, was determined. Sequence and phylogenetic analyses based on the sequences of eight genomic segments revealed that the isolate is phylogenetically related to the Y280-like sublineage.

Complete Genome Sequence of a Novel Reassortant H3N6 Avian Influenza Virus Isolated from Domestic Green-Winged Teal

An avian influenza virus strain, A/domestic green-winged teal/Hunan/2036/2007(H3N6) (DGW-T2036), was isolated from healthy domestic green-winged teals (Anas crecca) in Hunan Province, South China. All eight gene segments of the isolate were sequenced. Genomic analysis demonstrated that this H3N6 virus is a novel reassortant avian influenza virus with a gene constellation originating from multiple ancestors.

Environmental connections of novel avian-origin H7N9 influenza virus infection and virus adaptation to the human

A novel H7N9 influenza A virus has been discovered as the causative identity of the emerging acute respiratory infection cases in Shanghai, China. This virus has also been identified in cases of infection in the neighboring area Hangzhou City in Zhejiang Province. In this study, epidemiologic, clinical, and virological data from three patients in Hangzhou who were confirmed to be infected by the novel H7N9 influenza A virus were collected and analyzed. Human respiratory specimens and chicken feces from a contacted free market were tested for influenza virus by real-time reverse transcription PCR (RT-PCR) and sequencing. The clinical features of the three cases were similar featured with high fever and severe respiratory symptoms; however, only one of the patients died. A certain degree of diversity was observed among the three Hangzhou viruses sequenced from human samples compared with other reported H7N9 influenza A viruses. The sequences of the novel avian-origin H7N9 influenza viruses from Hangzhou City contained important amino acid substitutions related to human adaptation. One of the Hangzhou viruses had gained a novel amino acid substitution (Q226I) in the receptor binding region of hemagglutinin. More importantly, the virus sequenced from the chicken feces had a 627E substitution in the PB2 protein instead of the mammalian-adapted 627K substitution that was found in the PB2 proteins from the Hangzhou viruses from the three patients. Therefore, the newly-emerging H7N9 virus might be under adaptation pressure that will help it "jump" from avian to human hosts. The significance of these substitutions needs further exploration, with both laboratory experiments and extensive field surveillance.

Genome Sequence of a Novel Reassortant H3N6 Avian Influenza Virus from Domestic Mallard Ducks in Eastern China

Here, we report the complete genome sequence of an H3N6 avian influenza virus (AIV) isolated from domestic ducks in Jiangsu province of eastern China in 2010. Phylogenetic analysis showed that the H3N6 virus is a natural recombinant virus whose genes were derived from H3N8, H4N6, H6N6, H7N7, and H11N2 AIVs. This analysis will help to understand the molecular characteristics and evolution of the H3N6 influenza virus in eastern China.

Genome Sequence of a Novel Reassortant H3N2 Avian Influenza Virus from Domestic Mallard Ducks in Eastern China

The H3 subtype avian influenza virus (AIV) can provide genes for human influenza virus through gene reassortment, which raises great concerns in terms of its potential threat to human health. Here, we report the complete genome sequence of a novel H3N2 AIV isolated from domestic ducks in the Jiangsu province of eastern China in 2004, which is a natural recombinant virus whose genes are derived from H3N8, H5N1, H5N2, H11N2, H4N6, and H1N1 AIVs. This genome will help to understand the epidemiology and molecular characteristics of H3N2 influenza virus in eastern China.

Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments

Recombination plays an important role in shaping the genetic diversity of a number of DNA and RNA viruses. Although some recent studies have reported bioinformatic evidence of mosaic sequences in a variety of influenza A viruses, it remains controversial as to whether these represent bona fide natural recombination events or laboratory artifacts. Importantly, mosaic genome structures can create significant topological incongruence during phylogenetic analyses, which can mislead additional phylogeny-based molecular evolutionary analyses such as molecular clock dating, the detection of selection pressures and phylogeographic inference. As a result, there is a strong need for systematic screenings for mosaic structures within the influenza virus genome database. We used a combination of sequence-based and phylogeny-based methods to identify 388 mosaic influenza genomic segments, of which 332 are previously unreported and are significantly supported by phylogenetic methods. It is impossible, however, to ascertain whether these represent natural recombinants. To facilitate the future identification of recombinants, reference sets of non-recombinant sequences were selected for use in an automatic screening protocol for detecting mosaic sequences. Tests using real and simulated mosaic sequences indicate that our screening protocol is both sensitive (average >90%) and accurate (average >77%) enough to identify a range of different mosaic patterns. The relatively high prevalence of mosaic influenza virus sequences implies that efficient systematic screens, such as that proposed here, should be performed routinely to detect natural recombinant strains, potential laboratory artifacts, and sequencing contaminants either prior to sequences being deposited in GenBank or before they are used for phylogenetic analyses.

Complete Genomic Sequence of a Novel Reassortant H4N2 Avian Influenza Virus Isolated from Domestic Ducks in Jiangsu, China

Here, we report the complete genomic sequence of a novel reassortant H4N2 influenza virus isolated from domestic ducks in the Jiangsu province of China in 2011. Phylogenetic analysis showed that all the viral genes except for hemagglutinin (HA) were highly homologous to the clade 2.3.4 H5N2 viruses. The data suggest that genetic reassortment occurred between H4 and H5N2 avian influenza viruses, which highlights the role of domestic poultry as a reassortment vessel in China.

Complete Genome Sequence of a Canine-Origin H3N2 Feline Influenza Virus Isolated from Domestic Cats in South Korea

A canine-origin Korean H3N2 feline influenza virus (FIV), A/feline/Korea/01/2010 (H3N2), was isolated in 2010 from a dead cat with severe respiratory disease. Here, we report the first complete genome sequence of this virus, containing 3′ and 5′ noncoding regions, which will help elucidate the molecular basis of the pathogenesis, transmission, and evolution of FIV.

Emergence and characterisation of pandemic H1N1 influenza viruses in Hungarian swine herds

In 2010, two novel porcine H1N1 influenza viruses were isolated from pigs with influenza-like illness in Hungarian swine herds. Sequence and phylogenetic analysis of these strains revealed that they shared molecular features with the pandemic H1N1 influenza virus strains, which emerged globally during 2009. The PB2, HA and NA genes contained unique amino acid changes compared to the available new H1N1 influenza virus sequences of pig origin. Furthermore, the investigated strains could be separated with respect to parallel amino acid substitutions affecting the polymerase genes (PB2, PB1 and PA) and the nucleoprotein (NP) gene, supporting the proposed complementarities between these proteins, all required for the viral fitness. Molecular characterisation of two Hungarian human pandemic H1N1 isolates was also performed, so that we could compare contemporaneous strains of different host species origins. Shared molecular motifs in various genes of animal and human influenza strains suggested that the Hungarian porcine strains could have originated from humans through direct interspecies transmission. This study is among the few that support the natural human-to-pig transmission of the pandemic H1N1 influenza virus.

Resampling Nucleotide Sequences with Closest-Neighbor Trimming and Its Comparison to Other Methods

A large number of nucleotide sequences of various pathogens are available in public databases. The growth of the datasets has resulted in an enormous increase in computational costs. Moreover, due to differences in surveillance activities, the number of sequences found in databases varies from one country to another and from year to year. Therefore, it is important to study resampling methods to reduce the sampling bias. A novel algorithm–called the closest-neighbor trimming method–that resamples a given number of sequences from a large nucleotide sequence dataset was proposed. The performance of the proposed algorithm was compared with other algorithms by using the nucleotide sequences of human H3N2 influenza viruses. We compared the closest-neighbor trimming method with the naive hierarchical clustering algorithm and -medoids clustering algorithm. Genetic information accumulated in public databases contains sampling bias. The closest-neighbor trimming method can thin out densely sampled sequences from a given dataset. Since nucleotide sequences are among the most widely used materials for life sciences, we anticipate that our algorithm to various datasets will result in reducing sampling bias.

Complete Genome Sequence of a Natural Recombinant H9N2 Influenza Virus from Wild Birds in Republic of Korea

We report the complete genome sequence of a natural recombinant H9N2 avian influenza virus (AIV) that was isolated from a wild bird in the Republic of Korea in 2005. The genomic sequence and phylogenetic analyses showed that this virus contains six genes of North American lineage AIV and two genes of Eurasian lineage AIV. These data are beneficial for investigating the ecology and epidemiology of AIVs.

Nucleic Acid Sandwich Hybridization Assay with Quantum Dot-Induced Fluorescence Resonance Energy Transfer for Pathogen Detection

This paper reports a nucleic acid sandwich hybridization assay with a quantum dot (QD)-induced fluorescence resonance energy transfer (FRET) reporter system. Two label-free hemagglutinin H5 sequences (60-mer DNA and 630-nt cDNA fragment) of avian influenza viruses were used as the targets in this work. Two oligonucleotides (16 mers and 18 mers) that specifically recognize two separate but neighboring regions of the H5 sequences were served as the capturing and reporter probes, respectively. The capturing probe was conjugated to QD655 (donor) in a molar ratio of 10:1 (probe-to-QD), and the reporter probe was labeled with Alexa Fluor 660 dye (acceptor) during synthesis. The sandwich hybridization assay was done in a 20 μL transparent, adhesive frame-confined microchamber on a disposable, temperature-adjustable indium tin oxide (ITO) glass slide. The FRET signal in response to the sandwich hybridization was monitored by a homemade optical sensor comprising a single 400 nm UV light-emitting diode (LED), optical fibers, and a miniature 16-bit spectrophotometer. The target with a concentration ranging from 0.5 nM to 1 μM was successfully correlated with both QD emission decrease at 653 nm and dye emission increase at 690 nm. To sum up, this work is beneficial for developing a portable QD-based nucleic acid sensor for on-site pathogen detection.

Complete Genome Sequence of a Novel H4N1 Influenza Virus Isolated from a Pig in Central China

Pigs are proposed to be "mixing vessel" hosts that can produce genetically novel reassortant viruses with pandemic potential. The appearance of any novel influenza viruses among pigs should pose concerns for human health. Here, we report the complete genome sequence of a novel H4N1 influenza virus [A/Swine/HuBei/06/2009(H4N1)] isolated from a pig in Central China in 2009. The genomic sequence analysis indicates that this virus is a wholly avian-original influenza virus. Each gene may come from different avian influenza viruses outside mainland China, suggesting the role of migratory birds in the dispersal of influenza virus.

Complete Genome Sequence of a Novel Natural Recombinant H5N5 Influenza Virus from Ducks in Central China

We reported the complete genome sequence of an H5N5 avian influenza virus (AIV) that was first isolated from duck in central China in 2010. Genomic sequence and phylogenetic analyses showed that this virus was a recombinant between H5N1 AIV circulated in southeastern Asia and an N5 subtype influenza virus. These data are beneficial for investigating the epidemiology and ecology of AIVs in central China.

Complete Genome Sequence of an H10N5 Avian Influenza Virus Isolated from Pigs in Central China

An avian H10N5 influenza virus, A/swine/Hubei/10/2008/H10N5, was isolated from pigs in the Hubei Province of central China. Homology and phylogenetic analyses of all eight gene segments demonstrated that the strain was wholly of avian origin and closely homologous to the Eurasian lineage avian influenza virus. To our knowledge, this is the first report of interspecies transmission of an avian H10N5 influenza virus to domestic pigs under natural conditions.

Genome Sequence of a Monoreassortant H1N1 Swine Influenza Virus Isolated from a Pig in Hungary

The genome of a porcine H1N1 influenza A strain is reported in this study. The strain proved to be a monoreassortant strain with a typical porcine N1 gene on the genetic backbone of the pandemic H1N1 influenza A virus strain. Monitoring of descendants of the pandemic 2009 H1N1 strain is needed because of concerns that more-virulent strains may emerge in forthcoming epidemic seasons.

Insect cell-expressed hemagglutinin with CpG oligodeoxynucleotides plus alum as an adjuvant is a potential pandemic influenza vaccine candidate

Vaccination is the most effective method used to reduce the morbidity and mortality of influenza infections. However, as exemplified in the current swine-origin influenza virus (S-OIV) pandemic, the global manufacturing capacity of influenza vaccines is severely limited. In the present proof-of-concept study, we combined cell substrate selection and antigen engineering with adjuvant development to design a potential pandemic influenza vaccine candidate, in which CpG oligodeoxynucleotides (CpG-ODN) plus alum was used as a composite adjuvant to enhance the immunogenicity of insect cell-expressed recombinant hemagglutinin (rHA). Our candidate vaccine was found to be effective in inducing protective humoral as well as cellular immunity in mice and able to protect the immunized mice from related influenza virus challenge. If this candidate vaccine is validated in humans, vaccine development can be started immediately after the release of the first HA sequence of any pandemic influenza virus. Moreover, given the potential of large-scale manufacturing capacity of the recombinant antigen, in combination with the antigen-sparing effect of the composite adjuvant, this technology could be an invaluable asset in the fight against pandemic influenza.

Genome Sequence of a Natural Reassortant H5N2 Avian Influenza Virus from Domestic Mallard Ducks in Eastern China

Here, we report the genomic sequence of a Chinese reassortant H5N2 avian influenza virus which possessed the polybasic motif PLREKRRK-R/GL at the hemagglutinin cleavage site. Phylogenetic analysis showed that all eight genes were of the Eurasian lineage, five of which were highly homologous to the endemic clade 2.3.4 H5N1 viruses and their H5N5 reassortant descendants. These data suggested that novel multisubtypic NA reassortants bearing the H5N1 backbone could be generated through genetic reassortment in H5N1 circulating regions, which will help in understanding the evolution and segment reassortment mechanism of H5 subtype avian influenza viruses.