Chinese and global distribution of H9 subtype avian influenza viruses

Genomic Analysis and Surveillance of the Coronavirus Dominant in Ducks in China

The genetic diversity, evolution, distribution, and taxonomy of some coronaviruses dominant in birds other than chickens remain enigmatic. In this study we sequenced the genome of a newly identified coronavirus dominant in ducks (DdCoV), and performed a large-scale surveillance of coronaviruses in chickens and ducks using a conserved RT-PCR assay. The viral genome harbors a tandem repeat which is rare in vertebrate RNA viruses. The repeat is homologous to some proteins of various cellular organisms, but its origin remains unknown. Many substitutions, insertions, deletions, and some frameshifts and recombination events have occurred in the genome of the DdCoV, as compared with the coronavirus dominant in chickens (CdCoV). The distances between DdCoV and CdCoV are large enough to separate them into different species within the genus Gammacoronavirus. Our surveillance demonstrated that DdCoVs and CdCoVs belong to different lineages and occupy different ecological niches, further supporting that they should be classified into different species. Our surveillance also demonstrated that DdCoVs and CdCoVs are prevalent in live poultry markets in some regions of China. In conclusion, this study shed novel insight into the genetic diversity, evolution, distribution, and taxonomy of the coronaviruses circulating in chickens and ducks.

Isolation and full genome characterization of avian influenza subtype H9N2 from poultry respiratory disease outbreak in Egypt

Low pathogenic avian influenza virus of subtype H9N2 is panzootic in multiple avian species causing respiratory manifestations and severe economic losses. H9N2 co-circulate simultaneously with high pathogenic avian influenza virus subtype H5N1 in Egyptian chicken farms suggesting the possibility of reassortment. The aim of the present study was to isolate and characterize H9N2 from the recent outbreaks in chicken farms. Also the diversity of amantadine-resistant mutants among these isolates was tested by in situ ELISA and sequence analysis. Three influenza H9N2 viruses, designated A/chicken/Egypt/SCU8/2014, A/chicken/Egypt/SCU9/2014 and A/chicken/Egypt/SCU20/2014 were isolated from commercial broiler and broiler breeder chickens in specific pathogen free embryonated chicken eggs. The eight gene segments were amplified by RT-PCR, cloned, and subjected to full length sequencing. Phylogenetic analysis of these viruses revealed a close relationship between Egyptian, Middle Eastern and Israel isolates with an average of 96-99 % nucleotide homology and identified an ancestor relationship to low pathogenic H9N2 Quail/HK/G1/1997 prototype. The internal segments of the currently isolated viruses were derived from the same sub-lineage with no new evidence of reassortment. The three isolates were sensitive to amantadine as suggested by absence of mutations of M2 and confirmed by a phenotypic assay. In conclusion, avian influenza H9N2 virus is circulating in Egyptian chicken farms causing respiratory manifestations. Continuous monitoring of the molecular epidemiology and its impact on the virulence as well as emergence of new strains are necessary.

Isolation and phylogenetic analysis of hemagglutinin gene of H9N2 influenza viruses from chickens in South China from 2012 to 2013

As part of our ongoing influenza surveillance program in South China, 19 field strains of H9N2 subtype avian influenza viruses (AIVs) were isolated from dead or diseased chicken flocks in Guangdong province, South China, between 2012 and 2013. Hemagglutinin (HA) genes of these strains were sequenced and analyzed and phylogenic analysis showed that 12 of the 19 isolates belonged to the lineage h9.4.2.5, while the other seven belonged to h9.4.2.6. Specifically, we found that all of the viruses isolated in 2013 belonged to lineage h9.4.2.5. The lineage h9.4.2.5 viruses contained a PSRSSR↓GLF motif at HA cleavage site, while the lineage h9.4.2.6 viruses contained a PARSSR↓GLF at the same position. Most of the isolates in lineage h9.4.2.5 lost one potential glycosylation site at residues 200-202, and had an additional one at residues 295-297 in HA1. Notably, 19 isolates had an amino acid exchange (Q226L) in the receptor binding site, which indicated that the viruses had potential affinity of binding to human like receptor. The present study shows the importance of continuing surveillance of new H9N2 strains to better prepare for the next epidemic or pandemic outbreak of H9N2 AIV infections in chicken flocks.

PM2.5 in Beijing - temporal pattern and its association with influenza

BACKGROUND

Air pollution in Beijing, especially PM2.5, has received increasing attention in the past years. Despite Beijing being one of the most polluted cities in the world, there has still been a lack of quantitative research regarding the health impact of PM2.5 on the impact of diseases in Beijing. In this study, we aimed to characterize temporal pattern of PM2.5 and its potential association with human influenza in Beijing.

METHODS

Based on the data collected on hourly ambient PM2.5 from year 2008 to 2013 and on monthly human influenza cases from 2008 and 2011, we investigated temporal patterns of PM2.5 over the five-year period and utilized the wavelet approach to exploring the potential association between PM2.5 and influenza.

RESULTS

Our results found that ambient PM2.5 pollution was severe in Beijing with PM2.5 concentrations being significantly higher than the standards of the World Health Organization, the US EPA, and the Chinese EPA in the majority of days during the study period. Furthermore, PM2.5 concentrations in the winter heating seasons were higher than those in non-heating seasons despite high variations. We also found significant association between ambient PM2.5 peak and human influenza case increase with a delayed effect (e.g. delayed effect of PM2.5 on influenza).

CONCLUSIONS

Ambient PM2.5 concentrations were significantly associated with human influenza cases in Beijing, which have important implications for public health and environmental actions.

A clinical survey of common avian infectious diseases in China

Multiple common avian infectious diseases (CAIDs), namely, avian infectious diseases excluding highly pathogenic avian influenza and Newcastle disease, such as avian salmonellosis and coccidiosis, cause huge economic loss in poultry production and are of great significance in public health. However, they are usually not covered in the systems for reporting of animal diseases. Consequently, the distribution of CAIDs is not clear in many countries. Here, we report a clinical survey of CAIDs in China based on clinical diagnosis of eight veterinary clinics in 2011 and 2012. This survey provided the distribution data of viral, bacterial, and parasitic CAIDs in different types of avian flocks, seasons, and regions, data that are of great value in the research, prevention, and control of poultry diseases. This survey suggested that avian colibacillosis, infectious serositis in ducks caused by Riemerella anatipestifer, avian salmonellosis, fowl cholera, avian mycoplasmosis, avian aspergillosis, coccidiosis, low pathogenic avian influenza, infectious bronchitis, infectious bursal disease, and infectious laryngotracheitis are likely to be prevalent in the poultry in China.

Genetic variation and phylogenetic analysis of hemagglutinin genes of H9 avian influenza viruses isolated in China during 2010-2012

Genetic variation and phylogenetic relationships of H9 avian influenza viruses (AIVs) were analyzed based on hemagglutinin (HA) gene sequences of 84 Chinese H9 reference viruses recently available in GenBank, 3 widely used vaccine strains and 29 novel isolates. The novel isolates were obtained from vaccinated poultry flocks in 11 provinces of China during 2010 to 2012. The nucleotide homologies of HA genes of these isolates ranged from 87.8-99.8%, and from 89.8-93.2% as compared with the vaccine strains. Among the 29 novel isolates and the 84 reference viruses, 69.9% of the them belonged to the lineage h9.4.2.5 and had the dominant PSRSSR↓GLF motifs in the HA cleavage sites, while 27.4% of the them belonged to the newly emerging lineage h9.4.2.6 and had the dominant PARSSR↓GLF motifs, no consecutive basic amino acids insertion, showing the characteristic feature of low-pathogenic AIV. All the lineage h9.4.2.5 viruses and 75% of the lineage h9.4.2.6 viruses had the substitution Q226L (in H3 numbering). Additional potential glycosylation site at residues 313-315 (NCS) were found merely in all the lineage h9.4.2.5 viruses. Our results demonstrated that lineage h9.4.2.5 was more dominant than other lineages as it harbored more viruses that widely distributed in China in recent years. New lineage h9.4.2.6 previously existed mainly in South China had emerged in North China. Updated vaccine and increased veterinary biosecurity on poultry farms and trade markets are needed to prevent and control avian influenza.