[Study on the mutations within the whole genome of influenza virus subtype A/H3N2 strains circulated in Zhejiang province from 1998 to 2009].

OBJECTIVE: To analyze the consistency of evolution condition between HA gene and the whole genome of influenza virus subtype A/H3N2 strains isolated in Zhejiang province from 1998 to 2009, and to study the potential antigenic region on the whole genome. METHODS: The sequences of whole genome of 19 Zhejiang influenza virus isolates circulated from 1998 to 2009, which conserved by influenza laboratory of Zhejiang Provincial Centre for Disease Prevention and Control, were amplified using RT-PCR assays. The obtained sequences were used to conduct phylogenetic analysis with 10 contemporaneous vaccine strains. Three methods, including comparison of the amino acid substitutions, calculation of the entropy value and the filtering of positive selection sites, were used to confirm the mutable sites on each gene. RESULTS: The whole genome of influenza virus subtype A/H3N2 was 4466 amino acids in length, with 137 stable mutations. The 144, 158 aa of HA gene mutate four and three times respectively; 93, 143, 307, 370, 372 aa of NA gene and 450 aa of NP gene mutate twice, and there were 29% (12/41) and 77% (24/31) mutations of HA and NA genes occurred on the non-epitope regions respectively. Analysis of the entropy value suggest that many amino acid sites on the non-epitope regions were prone to mutation, including 3, 225, 361 aa of HA gene; 93, 143, 147, 150, 372 aa of NA gene; 113, 576, 586 aa of PB1 gene; 101,256, 382, 421, 437 aa of PA; 377, 450 aa of NP gene; 218 aa of M1 gene and 31 aa of M2 gene. CONCLUSION: Based on the whole genome of influenza virus subtype A/H3N2 strains isolated in Zhejiang province in 1998 to 2009, there may be several unknown or new antigen sites existing on the non-epitope regions of HA and NA genes and parts of internal genes. The phylogenetic tree constructed based on the complete sequence was more comprehensive than on the HA gene to reflect the genetic relationship and law of evolution among the influenza virus strains.

[Study on the complete sequence of CA24 variant isolated during the acute hemorrhagic conjunctivitis outbreaks in Zhejiang province during 2002 to 2010].

OBJECTIVE: To analyze the genetic characteristics of the complete sequence of coxsackievirus A24 variant (CA24v) isolated from acute hemorrhagic conjunctivitis (AHC) outbreaks in Zhejiang province during 2002 to 2010. METHODS: Complete sequences of CA24v epidemic strains isolated in different years were amplified under the RT-PCR assay, while the sequences of whole genome, VP1, and 3C region of Zhejiang strains were compared with epidemic strains isolated in other areas of China and abroad. RESULTS: The whole genome of Zhejiang CA24v strains isolated in 2002 and 2010 was 7456 - 7458 bp in length, encoding a polyglutamine protein which containing 2214 amino acid residues. There was a insertion with T on site 97 and 119 within 5'non-coding region between epidemic strain Zhejiang/08/10 and strains isolated in 2002. The rates of amino acid homology among Zhejiang/08/10 and other strains isolated since 2002 were between 94.7% and 100.0%. Compared with the representative strains circulated within the recent 60 years, the largest average amino acid variations had been occurred on region 2A and 3A, with the ratios as 8.4% and 7.3% respectively. The smallest variation happened in region 3D, with the ratio only as 1.9%. The rates of stable amino acid variation on the whole genome between strains isolated since 1987 and 2002 were 38 and 20. P-distance within groups appeared that region 3C was more stable than VP1 of strains isolated in 2002 - 2010, and the 3D of early strain Jamaica/10628/87 might have had a nature of recombination but not observed on those epidemic strains in recent years. CONCLUSION: Within the evolution of CA24v strains, the time course was more significant than the geographical differences. There had been sporadic epidemics of AHC caused by CA24v in Zhejiang province since 2002.

[Molecular evolution of two lineages related to influenza B virus based on HA1 gene].

OBJECTIVE: To study the evolutionary characteristics and rules of two lineages on influenza B virus. METHODS: A total of 126 HA1 sequences of strains isolated during 1940 to 2012 were downloaded from the GenBank. Time of the most recent common ancestor (TMRCA) and divergence of the two lineages were calculated based on the data from phylogenetic analysis of HA1 gene, using Bayesian Markov Chain Monte Carlo (Bayesian-MCMC) and molecular clock method. RESULTS: The average amino acid variant ratios were ranged from 5.4% to 10.2% within the strains of influenza B virus isolated during 1978 to 2010. Compared with the Victoria-like strains, all Yamagata-like strains showed an amino acid deletion at 163(th) site, while some of them showing a deletion at position 166. HA1 gene of influenza B virus seemed not have been affected by positive selection except a few sites. The evolutionary average rate on HA1 gene was 2.138×10(-3) substitutions/site/year (95% HPD: 1.833×10(-3) - 2.437×10(-3) substitutions/site/year). The estimated dates for TMRCA of the two lineages of influenza B virus could be dated back to 1971 (95% HPD: 1969 - 1972), while the divergence times of the two lineages were 1973 (95% HPD: 1971 - 1974) and 1977 (95% HPD: 1975 - 1978) respectively. CONCLUSION: Significant differences were found on HA1 gene between earlier and recent identified strains of Victoria and Yamagata lineage. Differences between the two lineages increased and showing the potential of dividing themselves into different subtypes in the future. More attention should be paid to these trends and the related epidemiological significance.

[Study on the genome sequence of measles viruses circulated in Zhejiang province during 1999 to 2011].

OBJECTIVE: To study the genetic variations between measles vaccine strain S191 and strains that circulated in Zhejiang province causing the epidemics during 1999 to 2011. METHODS: Complete sequence of the nine Zhejiang measles strains were amplified by RT-PCR assay. Products were sequenced and the obtained sequences were aligned and analyzed with vaccine strains S191 and the major epidemic strains isolated in foreign countries. RESULTS: The homology of amino acid among the nine Zhejiang strains were 98.77% - 99.89%. The strains were not affected by positive selection and the variations on each gene were still in random drift. Compared to vaccine strain S191, there were 135 to 159 amino acid changes in Zhejiang measles virus, in which 113 points were common variable positions, resulting in mutations on five glycosylation sites. At the nucleotide level, the biggest differences between the Zhejiang strains and the vaccine strain S191 were found on N gene, with the average divergent ratio as 5.5%, while the biggest one was P protein, in the amino acid level, with the average mutation rate as 7.7%. In addition, with the complete genome sequences, the genetic distance between Zhejiang epidemic strains and vaccine strains was greater than the distances between epidemic strains of genotype D(4), B(3) and vaccine strains (t = -9.76, P < 0.05; t = -12.39, P < 0.05). CONCLUSION: There were significant differences found in the each of the genes between Zhejiang epidemic strains and the vaccine strain S191. The differences between the current vaccine strains and H genotype epidemic strains were much larger than the differences between the vaccine and the foreign epidemic strains (genotype D(4), B(3)). Therefore, we should pay close attention to this trend, and to develop candidates for the development of vaccines, as early as possible.

[Traceability of the A/H3N2 virus borne influenza pandemic in Zhejiang province, 1998].

OBJECTIVE: To trace back to the influenza pandemic caused by A/H3N2 virus happened in Zhejiang province, 1998. METHODS: The whole genome of three isolates related to Zhejiang influenza virus was amplified through RT-PCR, and the identified sequences were aligned with the sequences downloaded from GenBank of the H3N2 strains which were circulating in other regions during 1995 to 1998. The crossing HAI titers of the reference strains were measured by HAI test and antigenic ratios were calculated. RESULTS: The Phylogenetic tree, constructed based on HA sequence showed that the dominant strains A/Zhejiang/11/98 and A/Zhejiang/18/98 were significant different from the isolates circulated in other regions during 1995 to 1996 and the strains isolated in the mainland of China, in 1997. Although the A/Zhejiang/11/98 and A/Zhejiang/18/98 strains were distributed in the same cluster with A/Sydney/5/97, the two strains were closer to the epidemic strains isolated in Hong Kong and New York in the later part of 1997. Based on HA1, NA and MP genes, A/Zhejiang/18/98 seemed to be the closest one to the Hong Kong epidemic strains, and the genetic distances between A/Zhejiang/18/98 and New York strains were shorter than that with A/Sydney/5/97 based on PA, HA and NS genes. There were only 1 - 3 amino acid differences between A/Zhejiang/18/98 and Hong Kong or New York strains, whereas 7 amino acid differences with A/Sydney/5/97, in which three were located in the antigenic determinant regions. Data from the crossing HAI test showed that the antigenic ratio between A/Zhejiang/18/98 and A/Sydney/5/97 had reached 2.0, indicating the antigenic difference to a certain extent. Additionally, the onset of the influenza epidemic during 1997 to 1998 also suggested the possible route of transmission related to this H3N2 virus. CONCLUSION: The influenza pandemic occurred in Zhejiang province in 1998 was possibly caused by the importation of a newly identified H3N2 influenza variant via Hong Kong and New York in late 1997.

[Study on the genome sequence of influenza virus subtype A/H3N2 strains circulated in Zhejiang province during 1998 to 2009].

OBJECTIVE: To analyze the relationship between influenza epidemic and genetic characteristic on the whole genome of influenza virus subtype A/H3N2 strains isolated in Zhejiang province during 1998 to 2009. METHODS: All of the eight genes from the 19 Zhejiang influenza virus isolates, circulated during 1998 to 2009, were amplified by RT-PCR and sequenced. The obtained sequences were aligned and analyzed with the vaccine strains being used in the last 10 years. RESULTS: The highest mutation happened within HA and NA genes and the amino acid divergent ratios were 13.98% and 10.00%. Amongst the six internal proteins, the amino acid divergent ratios of NP, M2 and NS1 were 6.43%, 6.19% and 3.48% respectively, and the others were lower than 3%. Other than the HA and NA genes, mutations were also observed on six internal genes of the strains isolated in those years when the influenza virus subtype A/H3N2 was widely circulating. Additionally, there had been an obvious genetic lag between vaccine strains recommended by WHO and the contemporary Zhejiang epidemic strains for many years. CONCLUSION: Besides on HA and NA genes, surveillance programs should also be covered mutations regarding the internal genes of influenza virus subtype A/H3N2 strains, in order to provide important information for forecasting and warning of a new round of influenza epidemic.

[Study on the differences on HA1 regions between epidemic strains and vaccine strains of influenza virus subtype A3 from 1988 to 2005].

OBJECTIVE: To study the differences between epidemic strains of influenza virus subtype A3 circulated in China and Occident in past 18 years, in genetic level, and vaccine strains recommended by WHO in corresponding time. METHODS: Amino acid sequences of HA1 regions of the epidemic strains, which circulated in China and Occident from 1988 to 2005, and the vaccine strains of influenza virus subtype A3 were compared by BioEdit and analyzed on the differences of HA1 and it's antigen determinants RESULTS: Differences between epidemic strains and vaccine strains recommended in corresponding year, both in HA1 and it' s antigen determinant regions, were obviously greater than that between epidemic strains and vaccine strains recommended in next round (P< 0.01). However, differences between epidemic strains in Occident and vaccine strains recommended in corresponding year were slightly greater than that between epidemic strains and vaccine strains recommended in next round and it was not marked (P >0.05). In addition, differences between epidemic strains and vaccine strains which being used for several years, whether in China or in Occident, constantly increased accompanying the used time prolonged. CONCLUSION: There was an obvious lag between vaccine strains recommended by WHO, analyzed in genetic level, and epidemic strains of influenza virus subtype A3 circulated in China.