Genetic Characterization of Continually Evolving Highly Pathogenic H5N6 Influenza Viruses in China, 2012–2016
H5N6 is a highly pathogenic avian influenza (HPAI) and a zoonotic disease that causes recurring endemics in East Asia. At least 155 H5N6 outbreaks, including 15 human infections, have been reported in China. These repeated outbreaks have increased concern that the H5N6 virus may cross over to humans and cause a pandemic. In February, 2016, peafowls in a breeding farm exhibited a highly contagious disease. Post-mortem examinations, including RT-PCR, and virus isolation, confirmed that the highly pathogenic H5N6 influenza virus was the causative agent, and the strain was named A/Pavo Cristatus/Jiangxi/JA1/2016. In animal experiments, it exhibited high pathogenicity in chickens and an estimated median lethal dose in mice of ~104.3 TCID50. A phylogenetic analysis showed that JA1/2016 was clustered in H5 clade 2.3.4.4. FG594-like H5N6 virus from Guangdong Province was the probable predecessor of JA1/2016, and the estimated divergence time was June 2014. Furthermore, we found that H5N6 influenza viruses can be classified into the two following groups: Group 1 and Group 2. Group 2 influenza viruses have not been detected since the end of 2014, whereas Group 1 influenza viruses have continually evolved and reassorted with the "gene pool" circulating in south China, resulting in the rise of novel subtypes of this influenza virus. An increase in the number of its identified hosts, the expanding range of its distribution, and the continual evolution of H5N6 AIVs enhance the risk that an H5N6 virus may spread to other continents and cause a pandemic.
[…] The phylogenetic analyses were performed using the listed gene sequences, which were acquired during a NCBI BLAST analysis. H5- and N6-subtype influenza virus sequences that were deposited from 2012 to 2016 were downloaded from the NCBI and/or the GISAID database. The reference sequences used for the H5-subtype influenza virus classifications were chosen based on guidance from OIE. All of the segmented sequence datasets were aligned using ClustalW 1.6. The alignment lengths for each gene segment dataset were as follows: PB2, 2,280 nt; PB1, 2,271 nt; PA, 2,151 nt; HA, 1692 nt; NP, 1482 nt; NA, 1,413 nt; M, 981 nt; and NS, 822 nt.Preliminary analyses were performed to estimate the best-fit nucleotide substitution model using jModeltest2 (Darriba et al., ). To estimate divergence times and rates of nucleotide substitutions, we used an uncorrelated relax-clock Bayesian Markov chain Monte Carlo method in BEAST v1.8.4 (Drummond et al., ). To determine which were the best-fit phylodynamic models, we performed different combinations of relaxed-clock models (i.e., exponential and log-normal models) and branch rate models (i.e., constant, exponential, expansion, and Bayersian SkyGrid models). The resultant *log files were imported into Tracer (v1.6) and then analyzed using model comparison analyses (AICM analysis; Drummond and Bouckaert, ). The best fit substitution models, relaxed-clock models, and tree models are listed in Supplementary Tables , . For each analysis, MCMC chains were run for 50 million iterations and sampled every 5 1000 iterations after a 10% burn-in to ensure an effective sample size was obtained for all posterior parameters, including the posterior, prior, likelihood, and meanRate (ESS > 200). For Clade 2.3.4.4 subtype H5 AIVs and N6 subtype AIVs analyses, the MCMC chains were run for 400 million iterations. Maximum clade credibility (MCC) trees were obtained from the MCMC tree samples using TreeAnnotator v1.8.4 (Drummond et al., ). The resulting trees were edited and illustrated using FigTree (v1.4.2; Morariu et al., ). […]
2017 Front Microbiol
DOI: 10.3389/fmicb.2017.00260
BLASTN, Clustal W, jModelTest, BEAST, FigTree
Homo sapiens, Pavo cristatus, Gallus gallus, Mus musculus
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link Influence of Autoinducer-2 (AI-2) in Cell-Free Supernatant of Salmonella Typhimurium in Gene Expression of S. Typhimurium link Global transcriptome analysis on Ankrd2 deficient or overexpressing differentiating primary myoblasts link Comparison of the Transcriptional Profiles of Melanocytes from Dark and Light Skinned Individuals under Basal Conditions and Following Ultraviolet-B Irradiation
link SNPrank link PhyDesign link BioCor
BUI THI LAN ANH
Vietnam-Russia Tropical Center
He Ting
link eggNOG link NCBI Epigenomics link DBTBS