Simultaneous Differential Detection of H5, H7, H9 and Nine NA Subtypes of Avian Influenza Viruses via a GeXP Assay

H5, H7 and H9 are the most important subtypes of avian influenza viruses (AIVs), and nine neuraminidase (NA) subtypes (N1-N9) of AIVs have been identified in poultry. A method that can simultaneously detect H5, H7, H9 and the nine NA subtypes of AIVs would save time and effort. In this study, 13 pairs of primers, including 12 pairs of subtype-specific primers for detecting particular subtypes (H5, H7, H9 and N1-N9) and one pair of universal primers for detecting all subtypes of AIVs, were designed and screened. The 13 pairs of primers were mixed in the same reaction, and the 13 target genes were simultaneously detected. A GeXP assay using all 13 pairs of primers to simultaneously detect H5, H7, H9 and the nine NA subtypes of AIVs was developed. The GeXP assay showed specific binding to the corresponding target genes for singlet and multiplex templates, and no cross-reactivity was observed between AIV subtypes and other related avian pathogens. Detection was observed even when only 102 copies of the 13 target genes were present. This study provides a high-throughput, rapid and labor-saving GeXP assay for the simultaneous rapid identification of three HA subtypes (H5, H7 and N9) and nine NA subtypes (N1-N9) of AIVs.

Reverse transcription recombinase-aided amplification assay for H5 subtype avian influenza virus

Background

The H5 subtype avian influenza virus (AIV) has caused huge economic losses to the poultry industry and is a threat to human health. A rapid and simple test is needed to confirm infection in suspected cases during disease outbreaks.

Methods

In this study, we developed a reverse transcription recombinase-aided amplification (RT-RAA) assay for the detection of H5 subtype AIV. Assays were performed at a single temperature (39 °C), and the results were obtained within 20 min.

Results

The assay showed no cross-detection with Newcastle disease virus or infectious bronchitis virus. The analytical sensitivity was 10³ RNA copies/μL at a 95% confidence interval according to probit regression analysis, with 100% specificity. Compared with published reverse transcription quantitative real-time polymerase chain reaction assays, the κ value of the RT-RAA assay in 420 avian clinical samples was 0.983 (p < 0.001). The sensitivity for avian clinical sample detection was 97.26% (95% CI, 89.56–99.52%), and the specificity was 100% (95% CI, 98.64–100%).

Conclusions

These results indicated that our RT-RAA assay may be a valuable tool for detecting H5 subtype AIV.

Genetically Diverse Highly Pathogenic Avian Influenza A(H5N1/H5N8) Viruses among Wild Waterfowl and Domestic Poultry, Japan, 2021

Genetic analyses of highly pathogenic avian influenza H5 subtype viruses isolated from the Izumi Plain, Japan, revealed cocirculation of 2 genetic groups of clade 2.3.4.4b viruses among migratory waterfowl. Our findings demonstrate that both continuous surveillance and timely information sharing of avian influenza viruses are valuable for rapid risk assessment.

H5 low pathogenic avian influenza viruses maintained in wild birds in China

Low pathogenic avian influenza virus, H5 or H7 subtype, possesses the potential capability to change to highly pathogenic variant, which damages wild waterfowl, domestic poultry, and mammalian hosts. In regular active surveillance of avian influenza virus from wild birds in China in 2020, we isolated six H5 avian influenza viruses, including one H5N2, two H5N3, and three H5N8. Phylogenetic analysis indicated that the H5N2 and H5N3 isolates clustered into Eurasian lineage, whereas the H5N8 viruses were originated in North America. The HA proteins of six viruses carried the cleavage-site motif PQRETR↓GLF, which indicated low pathogenicity of the viruses in chickens. However, the N30D, I43M, and T215A mutations in M1 protein and the P42S, I106M, and C138F residues changed in NS1 protein, implying all viruses could exhibit increased virulence in mice. Viral replication kinetics in mammalian cells demonstrated that the three representative viruses had the ability to replicate in both MDCK cells and A549 cells with low titers. Even though two of three representatives, WS/SX/S3-620/2020(H5N3) and ML/AH/A3-770/2020(H5N8), did not replicate and transmit efficiently in poultry (chickens), they did replicate and transmit efficiently in waterfowl (ducks). Viral pathogenicity in mice indicated that both H5N2 and H5N3 viruses are able to replicate in the nasal turbinates and lungs of mice without prior adaptation, while the H5N8 virus could not. The intercontinental and cross-species transmission of viruses may continuously exist in China, thereby providing constant opportunities for virus reassortment with local resident AIVs. Thus, it is crucial to continuously monitor migration routes for AIVs by systematic surveillance.

Comparative susceptibility of the common teal (Anas crecca) to infection with high pathogenic avian influenza virus strains isolated in Japan in 2004-2017

High pathogenic avian influenza viruses (HPAIVs) of the H5 subtype have spread in poultry and wild birds worldwide. Current studies have highlighted the association between the migration of wild birds and the spread of HPAIVs. However, virological studies examining responsible species of migratory birds to spread HPAIVs are limited. In Japan, the common teal (Anas crecca) arrives in great numbers for overwintering every autumn-spring season; therefore, we performed experimental infection using six H5 HPAIVs isolated in past outbreaks in Japan (A/chicken/Yamaguchi/7/2004 (H5N1), A/whooper swan/Akita/1/2008 (H5N1), A/mandarin duck/Miyazaki/22M-765/2011 (H5N1), A/duck/Chiba/26-372-48/2014 (H5N8), A/duck/Hyogo/1/2016 (H5N6) and A/mute swan/Shimane/3211A002/2017 (H5N6)) to evaluate the susceptibility of the species to HPAIV infection. The results illustrated that most birds in all experimental groups were infected by the strains, and they shed viruses for a prolonged period, in trachea than cloaca, without displaying distinctive clinical signs. In addition, comparative analysis using calculation value of total viral shedding during the experiment revealed that the birds shed viruses at above a certain level regardless of the differences of strains. These results suggested that the common teal could be a migratory bird species that disseminates viruses in the environment, thereby influencing HPAI outbreaks in wild birds in Japan.

Role of the Hemagglutinin Residue 227 in Immunogenicity of H5 and H7 Subtype Avian Influenza Vaccines in Chickens

Many H5 and H7 subtype avian influenza vaccines are poorly immunogenic in terms of inducing hemagglutination-inhibition (HI) antibody titers. Residue 227 (H3 numbering) in the receptor binding site in the hemagglutinin (HA) is critical for the detectability of HI antibodies induced by H5 influenza vaccines. However, whether the effect of residue 227 on immunogenicity can be generalized in different subtypes is unclear. In this study, the impact of HA residue 227 on immunogenicity of H5N1, H5N6, and H7N9 avian influenza vaccines was evaluated in chickens. Polymorphism analysis revealed that S227 is overwhelmingly dominant in HA of the H5N1 and H7N9 subtypes, whereas this amino acid is present in a small proportion of H5N6 viruses. The H5N1, H5N6, and H7N9 vaccines harboring S227 in HA induced relatively low HI titers at week 2 postimmunization (pi), and antibody titers increased at week 3 pi. S227N substitution in these vaccines consistently enhanced HI titers significantly. Another H5N6 vaccine harboring Q227 in HA elicited a robust HI antibody response, and Q227S substitution led to a significant drop of HI titers. Cross-HI testing against the wild-type and mutant viruses revealed that the amino acid at position 227 was associated with the detectability of HI titers induced by H5 and H7 avian influenza vaccines. The results indicate an important role of residue 227 in HA in immunogenicity of H5 and H7 subtype avian influenza vaccines in chickens. Our findings also provided useful information for vaccine seed virus selection and genetic engineering for immunogenicity enhancement of avian influenza vaccines.

Evolution and extensive reassortment of H5 influenza viruses isolated from wild birds in China over the past decade

Lethal infection of wild birds with different subtypes of H5 viruses continuously occur. To investigate the genetic evolution and pathogenicity of H5 viruses in wild birds, we performed a detailed genetic and biologic analysis of 27 viruses, including H5N1, H5N2, H5N6, and H5N8 subtypes, that were responsible for avian influenza outbreaks in wild birds in China over the past decade. We found that these 27 viruses, bearing different clades/subclades of HA, were complicated reassortants and formed 12 different genotypes. Ten of the viruses tested were highly pathogenic in chickens, but showed distinct pathotypes in ducks and mice. Five of these 10 viruses, which were all from clade2.3.4.4, could bind human-type receptors. Our findings reveal the diversity of the genetic and biologic properties of H5 viruses circulating in wild birds and highlight the need to carefully monitor and evaluate the risks these viruses pose to animal and public health.

Development of reverse transcription loop-mediated isothermal amplification assays for point-of-care testing of avian influenza virus subtype H5 and H9

Avian influenza (AIV) outbreaks can induce fatal human pulmonary infections in addition to economic losses to the poultry industry. In this study, we aimed to develop a rapid and sensitive point-of-care AIV test using loop-mediated isothermal amplification (LAMP) technology. We designed three sets of reverse transcription LAMP (RT-LAMP) primers targeting the matrix (M) and hemagglutinin (HA) genes of the H5 and H9 subtypes. RT-LAMP targeting the universal M gene was designed to screen for the presence of AIV and RT-LAMP assays targeting H5-HA and H9-HA were designed to discriminate between the H5 and H9 subtypes. All three RT-LAMP assays showed specific amplification results without nonspecific reactions. In terms of sensitivity, the detection limits of our RT-LAMP assays were 100 to 1,000 RNA copies per reaction, which were 10 times more sensitive than the detection limits of the reference reverse‒transcription polymerase chain reaction (RT-PCR) (1,000 to 10,000 RNA copies per reaction). The reaction time of our RT-LAMP assays was less than 30 min, which was approximately four times quicker than that of conventional RT-PCR. Altogether, these assays successfully detected the existence of AIV and discriminated between the H5 or H9 subtypes with higher sensitivity and less time than the conventional RT-PCR assay.

Estimating Risk to Responders Exposed to Avian Influenza A H5 and H7 Viruses in Poultry, United States, 2014-2017

In the United States, outbreaks of avian influenza H5 and H7 virus infections in poultry have raised concern about the risk for infections in humans. We reviewed the data collected during 2014-2017 and found no human infections among 4,555 exposed responders who were wearing protection.

Subpopulation Primers Essential for Exhaustive Detection of Diverse Hemagglutinin Genes of H5 Subtype Avian Influenza Viruses by Loop-Mediated Isothermal Amplification Method

Loop-mediated isothermal amplification (LAMP) is a potential screening test for avian influenza (AI), but its narrow detection spectrum limits its applications. To improve this narrow detection spectrum, 3 types of primers were compared for detection of diverse H5 subtype hemagglutinin (HA) genes. Four and 6 genes, of 10 genetically different H5 HA genes tested, were detected with S primers specific for A/duck/Tsukuba/9/2005 (H5N2) and with M primers (which contained mixed bases), respectively. In contrast, all 10 HA genes became positive with population primers (P primers) (a mixture of primers designed for each subpopulation of 2,202 HA genes). Our study indicated that the P primers for the forward inner primer (FIP) and backward inner primer (BIP) sites were essential for exhaustive detection, whereas those for the F3, forward loop (FL), backward loop (BL), and B3 sites were exchangeable with M primers. A base mismatch experiment demonstrated that HA genes with ≤2 base mismatches per primer site and ≤10 base mismatches per HA gene were amplifiable. Reverse transcription-LAMP was broadly reactive, specific for H5 subtype HA genes, and applicable to field samples, with the sensitivity of real-time PCR. The in silico analysis suggested that most H5 HA genes (2,586 positive genes/2,588 genes tested) registered in the GenBank database might be amplifiable. These results indicate that the use of subpopulation primers in LAMP allows exhaustive detection of diverse HA genes and H5 LAMP can be used as a reliable AI screening test in general diagnostic laboratories.

Phylogenetic Study of H5 Low Pathogenic Avian Influenza Viruses Detected in Wild Birds in Poland in 2010-2015

Introduction

The genomes of nine H5 subtypes of low pathogenic avian influenza virus (LPAIV) strains identified in wild birds in Poland between 2010 and 2015 were sequenced, and their phylogenetic relationship was determined.

Material and Methods

AIV genome segments were amplified by RT-PCR and the PCR products were sequenced using Sanger method. Phylogenetic trees were generated in MEGA6 software and digital genotyping approach was used to visualise the relationship between analysed strains and other AIVs.

Results

High genetic diversity was found in the analysed strains as multiple subgroups were identified in phylogenetic trees. In the HA tree, Polish strains clustered in two distinct subclades. High diversity was found for PB2, PB1, PA and NP, since 5-8 sublineages could be distinguished. Each strain had a different gene constellation, although relationship of as much as six out of eight gene segments was observed between two isolates. A relationship with poultry isolates was found for at least one segment of each Polish strain.

Conclusion

The genome configuration of tested strains indicates extensive reassortment, although the preference for specific gene constellation could be noticed. A significant relationship with isolates of poultry origin underlines the need for constant monitoring of the AIV gene pool circulating in the natural reservoir.

Establishment of the cross-clade antigen detection system for H5 subtype influenza viruses using peptide monoclonal antibodies specific for influenza virus H5 hemagglutinin

The H5 subtype of highly pathogenic avian influenza (H5 HPAI) viruses is a threat to both animal and human public health and has the potential to cause a serious future pandemic in humans. Thus, specific and rapid detection of H5 HPAI viruses is required for infection control in humans. To develop a simple and rapid diagnostic system to detect H5 HPAI viruses with high specificity and sensitivity, we attempted to prepare monoclonal antibodies (mAbs) that specifically recognize linear epitopes in hemagglutinin (HA) of H5 subtype viruses. Nine mAb clones were obtained from mice immunized with a synthetic partial peptide of H5 HA molecules conserved among various H5 HPAI viruses. The antigen-capture enzyme-linked immunosorbent assay using the most suitable combination of these mAbs, which bound specifically to lysed H5 HA under an optimized detergent condition, was specific for H5 viruses and could broadly detect H5 viruses in multiple different clades. Taken together, these peptide mAbs, which recognize linear epitopes in a highly conserved region of H5 HA, may be useful for specific and highly sensitive detection of H5 HPAI viruses and can help in the rapid diagnosis of human, avian, and animal H5 virus infections.

Infection Risk for Persons Exposed to Highly Pathogenic Avian Influenza A H5 Virus-Infected Birds, United States, December 2014-March 2015

Newly emerged highly pathogenic avian influenza (HPAI) A H5 viruses have caused outbreaks among birds in the United States. These viruses differ genetically from HPAI H5 viruses that previously caused human illness, most notably in Asia and Africa. To assess the risk for animal-to-human HPAI H5 virus transmission in the United States, we determined the number of persons with self-reported exposure to infected birds, the number with an acute respiratory infection (ARI) during a 10-day postexposure period, and the number with ARI who tested positive for influenza by real-time reverse transcription PCR or serologic testing for each outbreak during December 15, 2014-March 31, 2015. During 60 outbreaks in 13 states, a total of 164 persons were exposed to infected birds. ARI developed in 5 of these persons within 10 days of exposure. H5 influenza virus infection was not identified in any persons with ARI, suggesting a low risk for animal-to-human HPAI H5 virus transmission.

Nomenclature updates resulting from the evolution of avian influenza A(H5) virus clades 2.1.3.2a, 2.2.1, and 2.3.4 during 2013-2014

Aim

The A/goose/Guangdong/1/96-like hemagglutinin (HA) genes of highly pathogenic avian influenza (HPAI) A(H5) viruses have continued to rapidly evolve since the most recent update to the H5 clade nomenclature by the WHO/OIE/FAO H5N1 Evolution Working Group. New clades diverging beyond established boundaries need to be identified and designated accordingly.

Method

Hemagglutinin sequences deposited in publicly accessible databases up to December 31, 2014, were analyzed by phylogenetic and average pairwise distance methods to identify new clades that merit nomenclature changes.

Results

Three new clade designations were recommended based on division of clade 2·1·3·2a (Indonesia), 2·2·1 (Egypt), and 2·3·4 (widespread detection in Asia, Europe, and North America) that includes newly emergent HPAI virus subtypes H5N2, H5N3, H5N5, H5N6, and H5N8.

Conclusion

Continued global surveillance for HPAI A(H5) viruses in all host species and timely reporting of sequence data will be critical to quickly identify new clades and assess their potential impact on human and animal health.

Estimation of the sensitivity of the surveillance system for avian influenza in the western region of Cuba

Although avian influenza (AI) virus of H5 and H7 subtypes has the potential to mutate to a highly pathogenic form and cause very high mortalities in some poultry species, most AI infections in poultry are due to low pathogenic AI (LPAI). Hence serological surveys, coupled with passive surveillance activities, are essential to detect sub-clinical infections by LPAI viruses, H5 and H7 subtypes. However the proper planning of an active surveillance system should be based on a careful estimation of its performance. Therefore, the sensitivity of the active surveillance system for AI in the western region of Cuba was assessed by a stochastic model quantifying the probability of revealing at least one animal infected by H5 or H7 subtype. The diagnostic sensitivity of the haemagglutination inhibition assay and different levels of within-flock prevalence (5%, 12% and 30%) were considered. The sensitivity of the surveillance system was then assessed under five different samples size scenarios: testing 20, 30, 40, 50 or 60 animals in each flock. Poultry flock sites in the western region of Cuba with a size ranging from 10,000 to 335,000 birds were included in the study.

Evidence for Chlamydiaceae and Parachlamydiaceae in a wild boar (Sus scrofa) population in Italy

Conjunctival swabs from 44 free-living wild boars culled during a demographic control programme applied in a Regional Park located in the Northern Italy were examined by 16S rRNA encoding gene nested PCR. In total, 22 (50%) wild boars were PCR positive. Sequencing of the amplicons identified Chlamydia suis and Chlamydia pecorum in 12 and 5 samples, respectively. For one sample found PCR positive, the nucleotide sequence could not be determined. Four conjunctival samples showed ≥ 92% sequence similarities to 16S rRNA sequences from Chlamydia-like organisms, as did large intestine, uterus, and vaginal swabs from the same four animals. Amoeba DNA was found in one Chlamydia-like organism positive conjunctival swab. To our knowledge, this is the first detection of members of the Parachlamydiaceae family in wild boars, confirming a large animal host range for Chlamydia-like organisms.