Pdm09 virus outbreak occurred in Mainland China in May 2009, a few months later, the prevalence of seasonal H1N1(sH1N1) influenza virus that already circulated in human for tens of years began to decline and disappeared afterwards. To identify the reason for the rapid decline of sH1N1 in mainland China, we sequenced the HA1 of sH1N1 during 2006-2011, and then analyzed the selective pressure in different phases. Our results showed before Pdm09 outbreak, the omega value was 0. 36 while after Pdm09 outbreak the omega value was 0. 28 and significant difference (t test, P<0. 05) was identified. We concluded that sH1N1 obtained stronger purifying selection after Pdm09 outbreak in China. This might one of the major reasons causing the disappearance of sH1N1 in human.
China ; Humans ; Influenza A Virus, H1N1 Subtype ; classification ; genetics ; isolation & purification ; Influenza, Human ; virology ; Phylogeny ; Seasons ; Selection, Genetic

The clinical throat swab specimen of an imported suspected case of influenza A (H1N1) was detec ted with real-time PCR, RT-PCR and subsequently confirmed by gene sequencing. The presence of influ enza A (H1N1) virus confirmed the first case with A (H1N1) infection in Mainland China.
China ; Humans ; Influenza A Virus, H1N1 Subtype ; classification ; genetics ; isolation & purification ; Influenza, Human ; virology ; Molecular Sequence Data ; Phylogeny

OBJECTIVETo analyze the type and subtype distribution of influenza virus and the genetic evolution of hemagglutinin (HA) in Shanghai area during 2004 to 2008.

METHODSAll 962 throat swabs were collected from influenza-like patients in 5 influenza sentry hospitals and influenza outbreaks. Influenza viruses were isolated in MDCK cell lines, and then viral types and subtypes were identified. The HA of influenza A isolates selected by outbreak or sporadic patients in different areas and epidemic seasons were sequenced and analyzed by phylogenetic trees.

RESULTSA/H3N2, accounting for 54.9% (162/295), was the dominate subtype in recent years, but less popular in the end of 2005 to the middle of 2006 with 0% (0/16)and 23.5% (8/34) of positive specimen, respectively. There were more A/H1N1 isolates in 2005 - 2006 with 21.4% (12/56), 43.8% (7/16) and 76.5% (26/34) of positive specimen, respectively, but declined obviously in 2007 - 2008 accounting for only 0% (0/44) and 5.0% (7/139). Influenza B virus was more popular in 2004 to 2005 with 42.9% (24/56) and 56.2% (9/16), respectively, and not isolated from 2006 to 2007, then increased in 2008 accounting for 34.5% (48/139). Phylogenetic tree of HA showed that A/H1N1 isolates in the same year clustered from 2005 to 2008, and most A/H3N2 isolated were homologous in the same year during 2004 - 2008 while some were inserted to the clusters of near years and more distinguished sequences appeared. A/H1N1 and A/H3N2 isolates were all similar to the vaccine strains recommended by WHO.

CONCLUSIONThe distribution of influenza type and subtype kept on changing each year, but A/H3N2 dominated in most years. A/H1N1 and A/H3N2 in the same year clustered, but some A/H3N2 of near years were and evolved faster with more distinguished strains appeared in same interval. Generally, HA of influenza A isolates in Shanghai during 2004 to 2008 were similar to the WHO reference strains.

China ; epidemiology ; Evolution, Molecular ; Hemagglutinin Glycoproteins, Influenza Virus ; genetics ; Humans ; Influenza A Virus, H1N1 Subtype ; classification ; genetics ; isolation & purification ; Influenza A Virus, H3N2 Subtype ; classification ; genetics ; isolation & purification ; Influenza, Human ; epidemiology ; virology

OBJECTIVETo isolate and identify the influenza virus that caused four influenza-like-illness outbreaks in Jining city of Shandong Province in 2009 and analyze the genetic characteristics of hemagglutinin (HA) and neuraminidase (NA) gene, the variation of these genes were studied.

METHODS34 nasopharyngeal swabs from fever patients of four influenza-like-illness outbreaks were collected and diagnosed by real time quantitative RT-PCR method. The positive samples were incubated and cultured for virus. HA and NA genes of isolated pandemic influenza A (H1N1) virus were sequenced, the homology analysis was done with DNAStar software and the genetic evolution and amino acid substitutions were performed with Mega 4.0 software. The sequences were compared with WHO recommended vaccine virus, native reference virus.

RESULTSSeventeen of 34 nasopharyngeal swabs were positive, 11 pandemic influenza A (H1N1) viruses were isolated and HA and NA genes of 7 strains were sequenced. Phylogenetic analysis for hemagglutinin and neuraminidase gene of Shandong outbreak strains showed that there were 98.4% - 99.6% and 99.2% - 100.0% sequence identity. Compared with WHO-recommended vaccine strain, the reference virus in mainland China strain, eleven amino acids were changed for HA protein, including position 38, 40, 56, 90, 100, 145, 172, 173, 220, 303 and 338, and 38, 40, 303 of HA protein were located in the antigenic determination C cluster, 172, 173 in the D cluster, 56 in the E cluster, site 40 of HA protein were glycosylated. In NA protein, seven amino acids were changed, including position 80, 106, 241, 248, 351, 369 and 386, site 40 of NA protein were glycosylated. No mutations of 275 in NA protein were found.

CONCLUSIONThe HA and NA genes of the epidemic strains showed high homology, some mutations in the HA and NA proteins were found, the antigenic site and glycosylation site of some strains were changed during the epidemic process.

China ; epidemiology ; Disease Outbreaks ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza Virus ; genetics ; Humans ; Influenza A Virus, H1N1 Subtype ; classification ; genetics ; isolation & purification ; Influenza, Human ; epidemiology ; virology ; Neuraminidase ; genetics

BACKGROUNDThrough the analysis of internal genes of viruses to understand whether the internal genes of two strains of swine influenza A(H1N1) virus contain the gene segment deriving from avian influenza A viruses, and whether the reassortment of the internal genes occurred between swine H1N1 and swine H9N2 viruses.

METHODSViruses were passaged in embryonated hen eggs and virion RNA was extracted from allantoic fluids and reverse transcribed to synthesize cDNA. cDNA was amplified by PCR and the PCR product was purified with a purification kit. Afterwards, RNA sequence analysis was performed by dideoxynucleotide chain termination and a cloning method. Finally, phylogenetic analysis of the sequencing data was performed with MegAlign (version 1.03).

RESULTSAll the six, but PB2 gene segment internal gene segments were the same between A/swine/Beijing/1/2002(H1N1) and A/Swine/Beijing/3/2002(H1N1) viruses. Whereas all the six internal gene segments in two trains of swine (H1N1) virus were similar to those of swine H1N1 viruses, but different from those of classical strain of swine (H1N1) virus.

CONCLUSIONTwo strains of Beijing swine H1N1 influenza A virus were not reassortant, All the six internal gene segments were closely related to swine influenza A (H1N1) viruses.

Animals ; Chick Embryo ; DNA, Complementary ; chemistry ; genetics ; Influenza A Virus, H1N1 Subtype ; classification ; genetics ; isolation & purification ; Influenza A Virus, H9N2 Subtype ; genetics ; Phylogeny ; RNA, Viral ; genetics ; Reassortant Viruses ; genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Swine ; virology

In order to visually detect H1, N1 and N2 subtype of avian influenza virus (AIV), three reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays were developed. According to the sequences of AIV gene available in GenBank, three degenerate primer sets specific to HA gene of H1 subtype AIV, NA gene of N1 and N2 subtype AIV were designed, and the reaction conditions were optimized. The results showed that all the assays had no cross-reaction with other subtype AIV and other avian respiratory pathogens, and the detection limit was higher than that of conventional RT-PCR. These assays were performed in water bath within 50 minutes. Without opening tube, the amplification result could be directly determined by inspecting the color change of reaction system as long as these assays were fin-ished. Fourteen specimens of H1N1 subtype and eight specimens of H1N2 subtype of AIV were identified from the 120 clinical samples by RT-LAMP assays developed, which was consistent with that of virus isolation. These results suggested that the three newly developed RT-LAMEP assays were simple, specific and sensitive and had potential for visual detection of H1, N1 and N2 subtype of AIV in field.
Animals ; Chickens ; DNA Primers ; genetics ; Ducks ; Influenza A Virus, H1N1 Subtype ; classification ; genetics ; isolation & purification ; Influenza A Virus, H1N2 Subtype ; classification ; genetics ; isolation & purification ; Influenza A virus ; classification ; genetics ; isolation & purification ; Influenza in Birds ; diagnosis ; virology ; Nucleic Acid Amplification Techniques ; methods ; Poultry Diseases ; diagnosis ; virology ; Reverse Transcription ; Turkeys

To analyze influenza pathogen spectrum in Yunnan province during 2009-2014 years, and analyze HA and NA genes of influenza A H1N1. Analysis was made on the monitoring date of influenza cases in Yunnan province in recent 6 years, 23 strains of influenza virus of HA and NA gene was sequenced and analyzed by MEGA 5 software to construct phylogenetic tree. 4 times of influenza AH1N1 epidemic peak were monitored from 2009-2014 years in Yunnan Province, as the nucleic acid detection results of influenza A H1N1 accounted for 28.8% of the total. The sequencing result showed that HA and NA gene were divided into 3 groups, one was detected with H275Y mutation strains. Influenza A H1N1 is one of the important subtypes in Yunnan province and their genes have divided into three branches during the period of 2009-2014 years, the vast majority of influenza a H1N1 are still sensitive to neuraminidase inhibitors.
China ; epidemiology ; Hemagglutinin Glycoproteins, Influenza Virus ; genetics ; metabolism ; Humans ; Influenza A Virus, H1N1 Subtype ; classification ; enzymology ; genetics ; isolation & purification ; Influenza, Human ; epidemiology ; virology ; Molecular Sequence Data ; Mutation ; Neuraminidase ; genetics ; metabolism ; Phylogeny ; Viral Proteins ; genetics ; metabolism

OBJECTIVEIn order to provide a scientific basis for influenza prevention and control, analyzing the epidemic characteristics and laws of influenza outbreaks in Xuzhou area during 2005-2011.

METHODUsing fluorescent-PCR method to detect influenza virus nucleic acid on Nasopharyngeal swab specimens collected from influenza outbreak cases during 2005-2011 and fast classifying influenza virus A1 (H1N1), A3 (H3N2), new H1N1 BV (Victoria) and BY (Yamagate) on subtypes. At the same time, isolating the influenza virus with MDCK cells, and sending them to the National Influenza Center for review, after the preliminary identification of the isolated influenza virus.

RESULTSDuring 2005-2011, there are 53 influenza outbreaks in Xuzhou area, which caused by influenza virus subtype BV accounting for 26.42% (14/53), A3 accounting for 49.1% (26/53), A3 and A1 mixture accounting for 3.77% (2/53) and the new H1N1 accounting for 20.75% (11/53). The outbreaks in 2007 and 2009 mainly caused by A3, and show that the winter spring (January) and summer autumn (September) as two popular peaks during 2005-2011; BV mainly causes the outbreaks from Feb. to Jun.

CONCLUSIONIn Xuzhou area, since the winter of 2005, influenza virus subtype BV, the A3, and new H1N1 has alternately as mainly predominant strain, caused local influenza outbreaks. In which BV has increased trend year by year during 2005-2011. The students in primary and secondary schools are the major crowd of influenza outbreaks. Fluorescent-PCR detection methods could be a preferred method for reliable and rapid diagnostic of epidemic influenza outbreaks.

Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; China ; epidemiology ; Disease Outbreaks ; Female ; Humans ; Influenza A Virus, H1N1 Subtype ; classification ; genetics ; isolation & purification ; Influenza A Virus, H3N2 Subtype ; classification ; genetics ; isolation & purification ; Influenza A virus ; classification ; genetics ; isolation & purification ; Influenza, Human ; epidemiology ; virology ; Male ; Middle Aged ; Public Health Surveillance ; Seasons ; Young Adult

OBJECTIVETo investigate the prevalence and subtypes of influenza viruses in Xuzhou city from 2005 to 2011 and to provide the scientific supports for influenza prevention and control in this religion.

METHODSThe throat swab samples were collected from the influenza-like cases from national influenza like illness sentinel hospital in Xuzhou. The samples were used for influenza virus isolation and identification, sent on the national flu center to confirm according to the "national influenza surveillance program" and "influenza virus and experimental technology".

RESULTSFrom Oct. 2005 to Dec. 2011, a total of 9561 swab specimens were collected in which 1152 strains were identified for influenza viruses with total isolated rate of 12.0%. Among these strains, 708 strains were A1 (H1N1) subtype (14.2%), 466 strains were A3 (H3N2) subtype (40.5%), 78 strains were new H1N1 subtype (6.8%), 362 strains were BV (Victoia) subtype (31.4%) and 82 strains were BY (Yamagate) subtype (7.1%). The top detection rate (25.9%) arose in 2007, secondary detection rate (17.4%) occurred at 2009 and the lowest one (2.3%) appeared in 2011. From the winter of 2005 to the spring of 2006 A1 (H1N1) subtype had appeared as predominant strains but in the winter of 2006 the predominant strains were BV subtype. It changed to A3 subtype in 2007 to 2009 and the other three dominant strains were A1, BV and BY in 2008. In the winter of 2009, both A3 (H3N2) and new H1N1 subtype were predominant strains. BV subtype was predominant strains in 2010 to 2011. The prevalence of A3 subtype appeared in all the year while prevalence of BV only arose in the spring and winter. So the detection rate was high in January (34.4%) but low in August (2.2%). The influenza population is correlated with age, the highest detection rate arose in 5-age group and the lowest detection rate appeared in 25-age group.

CONCLUSIONInfluenza subtype A1, A3, New H1N1 are all appeared as predominant strains in Xuzhou city from 2005 to 2010. Besides, the prevalence of BV subtype is stronger in recently.

Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; China ; epidemiology ; Female ; Humans ; Infant ; Influenza A Virus, H1N1 Subtype ; classification ; genetics ; isolation & purification ; Influenza A Virus, H3N2 Subtype ; classification ; genetics ; isolation & purification ; Influenza A virus ; classification ; genetics ; isolation & purification ; Influenza, Human ; epidemiology ; virology ; Male ; Middle Aged ; Public Health Surveillance ; Seasons ; Young Adult

OBJECTIVETo characterize the prevalence and antigenic drift of influenza A viruses isolated during the period from 2001 to 2005 in infants and young children in Beijing.

METHODSMDCK cell culture, indirect immunofluorescence assay (IFA) and hemagglutination inhibition (HI) assay were used to isolate and identify type A influenza viruses (H1N1 and H3N2) from clinical samples collected from outpatients and inpatients who visited the Affiliated Children's Hospital because of acute respiratory infections from Oct. 2001 to Aug. 2005. The HA1 regions of hemagglutinin gene of H3N2 isolates were amplified by using RT-PCR followed by sequencing.

RESULTSOut of 7338 clinical samples collected during this surveillance period, 347 (4.7%) were positive for influenza A viruses, including 48 (13.8%) of H1N1, 273 (78.7%) of H3N2 and 26 (7.5%) of subtype-unidentified influenza A viruses. Although there was a prevalence season of influenza A from October each year to April of next year during the 2001-2004 period, it was worth noting that a consecutive influenza A activity was detected from Aug. 2004 to Aug. 2005, when some influenza A viruses were detected even in summer. The positive rate of H3N2 was 14.2% in August, 2005, which was equal to that of the peak season of 2003-2004. H3N2 were predominant in most of the influenza seasons during the surveillance period, and H1N1 was detected only in the influenza seasons of the 2001-2002 and 2004-2005 along with H3N2. The positive rates for both H3N2 and H1N1 were higher in specimens from outpatients than those from inpatients. A total of 46.6% (110/236) of the H3N2 were detected from children younger than 2 years of age, and 14.0% (33/236) were from children older than 5 years, whereas, more H1N1 was found in children older than 5 years (48.0%, 12/31) than in those younger than 2 years (6.5%, 2/31) during a period from Nov. 2003 to Aug. 2005. Sequence analysis of the HA1 regions of hemagglutinin of H3N2 isolated in a series of years revealed amino acid changes in the HA1 domain of H3N2 isolates in the antigenic sites (A-E) each year.

CONCLUSIONH3N2 and H1N1 prevailed in each influenza season during the surveillance period in Beijing, and H3N2 strains were predominant. The data from all-year around surveillance of influenza in Beijing indicate that continuous surveillance throughout a year and use of both antigenic and molecular analysis will be more helpful for early identification of any antigenic variants as well as prevention and control of influenza by promoting development of vaccines.

Age Factors ; Animals ; Antigenic Variation ; genetics ; Cell Culture Techniques ; Child ; Child, Preschool ; China ; epidemiology ; Dogs ; Female ; Hemagglutinin Glycoproteins, Influenza Virus ; genetics ; Humans ; Infant ; Influenza A Virus, H1N1 Subtype ; isolation & purification ; Influenza A Virus, H3N2 Subtype ; isolation & purification ; Influenza A virus ; classification ; genetics ; isolation & purification ; Influenza, Human ; virology ; Inpatients ; Male ; Outpatients ; Prevalence ; Respiratory Tract Infections ; virology ; Retrospective Studies ; Reverse Transcriptase Polymerase Chain Reaction ; Time Factors