1.Evolutionary characterization of HA1 of influenza H1N1 hemagglutinin gene surveyed in 1981-2005 in China.
Jia-Huai ZHANG ; Hong XU ; Ye ZHANG ; Xiang ZHAO ; Jun-Feng GUO ; Yu LAN ; Yue-Long SHU
Chinese Journal of Virology 2007;23(5):350-355
To understand the evolutionary characterization of HA1 of H1N1 influenza virus HA gene circulaing from 1981 to 2005 in China, viral RNAs of 370 H1N1 strains were extracted and transcribed into cDNA by reverse transcriptase and amplified by PCR. The products of PCR were sequenced. The sequences were analyzed through biometic software. The results showed that all the four antigenic sites were mutated, bigger change occurred on the Sb and Ca sites; the 130 loop of receptor binding sites(RBS) of HA1 amino acid deleted at the 134th site in 1991 firstly, then the number of the deleted strains were increasing, since 2000, all the strains had deleted at the 134th site, and simultaneously, the amino acid at 137th site was substituted by S for T. The change of HA1 glycosylation sites was found and 7 sites kept stable from 2000 to 2005. The H1N1 strains of the same year almost clustered in the same group on the phylogenetic tree and were irrelevant to virus isolated time and area. There appeared two groups of 2005 H1N1 virus strains that differed in time of virus isolation.
China
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Genes, Viral
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Hemagglutinin Glycoproteins, Influenza Virus
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genetics
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Influenza A Virus, H1N1 Subtype
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genetics
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Phylogeny
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Time Factors
2.Genetic characteristics of the first human infection with the G4 genotype eurasian avian-like H1N1 swine influenza virus in Shaanxi Province,China.
Long QIN ; Jun Jun ZHANG ; Bin CHEN ; Shi Feng WANG ; Peng Bo YU
Chinese Journal of Preventive Medicine 2023;57(9):1434-1439
Objective: To analyze the genetic characteristics of the first human infection with the G4 genotype of Eurasian avian H1N1 swine influenza virus (EA H1N1 SIV) in Shaanxi Province. Methods: The patient's throat swab samples were collected, and MDCK cells were inoculated for virus isolation to obtain the virus strain. The whole genome deep sequencing method was used to obtain the eight gene segments of the isolated strain. The nucleotide homology analysis was conducted through the Blast program in the GenBank database, and a phylogenetic tree was constructed to analyze the genetic characteristics of the virus. Results: The throat swab specimens of the case were confirmed as EA H1N1 SIV in the laboratory, and the isolated strain was named A/Shaanxi-Weicheng/1351/2022(H1N1v). Homology analysis found that the PB2, NP, HA, NA, and M genes of this isolate had the highest nucleotide homology with A/swing/Beijing/0301/2018 (H1N1), about 98.29%, 98.73%, 97.41%, 97.52%, and 99.08%, respectively. The phylogenetic tree showed that the isolate belonged to G4 genotype EA H1N1 SIV, with PB2, PB1, PA, NP and M genes from pdm/09 H1N1, HA and NA genes from EA H1N1, and NS gene from Triple-reassortant H1N1. The cleavage site of the HA protein was IPSIQSR↓G, which was the molecular characteristic of the low pathogenic influenza virus. No amino acid mutations associated with neuraminidase inhibitors were found in the NA protein. PB2 protein 701N mutation, PA protein P224S mutation, NP protein Q357K mutation, M protein P41A mutation, and NS protein 92D all indicated its enhanced adaptability to mammals. Conclusion: The patient is the first human infection with G4 genotype EA H1N1 SIV in Shaanxi province. The virus is low pathogenic, but its adaptability to mammals is enhanced. Therefore, it is necessary to strengthen the monitoring of such SIVs.
Swine
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Humans
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Animals
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Influenza A Virus, H1N1 Subtype/genetics*
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Phylogeny
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Genotype
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Influenza A virus
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China
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Birds
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Mammals
3.Genetic characteristics of the first human infection with the G4 genotype eurasian avian-like H1N1 swine influenza virus in Shaanxi Province,China.
Long QIN ; Jun Jun ZHANG ; Bin CHEN ; Shi Feng WANG ; Peng Bo YU
Chinese Journal of Preventive Medicine 2023;57(9):1434-1439
Objective: To analyze the genetic characteristics of the first human infection with the G4 genotype of Eurasian avian H1N1 swine influenza virus (EA H1N1 SIV) in Shaanxi Province. Methods: The patient's throat swab samples were collected, and MDCK cells were inoculated for virus isolation to obtain the virus strain. The whole genome deep sequencing method was used to obtain the eight gene segments of the isolated strain. The nucleotide homology analysis was conducted through the Blast program in the GenBank database, and a phylogenetic tree was constructed to analyze the genetic characteristics of the virus. Results: The throat swab specimens of the case were confirmed as EA H1N1 SIV in the laboratory, and the isolated strain was named A/Shaanxi-Weicheng/1351/2022(H1N1v). Homology analysis found that the PB2, NP, HA, NA, and M genes of this isolate had the highest nucleotide homology with A/swing/Beijing/0301/2018 (H1N1), about 98.29%, 98.73%, 97.41%, 97.52%, and 99.08%, respectively. The phylogenetic tree showed that the isolate belonged to G4 genotype EA H1N1 SIV, with PB2, PB1, PA, NP and M genes from pdm/09 H1N1, HA and NA genes from EA H1N1, and NS gene from Triple-reassortant H1N1. The cleavage site of the HA protein was IPSIQSR↓G, which was the molecular characteristic of the low pathogenic influenza virus. No amino acid mutations associated with neuraminidase inhibitors were found in the NA protein. PB2 protein 701N mutation, PA protein P224S mutation, NP protein Q357K mutation, M protein P41A mutation, and NS protein 92D all indicated its enhanced adaptability to mammals. Conclusion: The patient is the first human infection with G4 genotype EA H1N1 SIV in Shaanxi province. The virus is low pathogenic, but its adaptability to mammals is enhanced. Therefore, it is necessary to strengthen the monitoring of such SIVs.
Swine
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Humans
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Animals
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Influenza A Virus, H1N1 Subtype/genetics*
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Phylogeny
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Genotype
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Influenza A virus
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China
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Birds
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Mammals
6.Epidemiology of 1977 Russian flu.
Yan GAO ; Shan-Hua SUN ; Wei LIU ; Yuan-Yuan YAO ; Tian BAI ; Xi-Yan LI ; Cui-Ling XU ; Yuan-Ji GUO ; De-Xin LI ; Yue-Long SHU
Chinese Journal of Virology 2009;25 Suppl():36-38
7.Discrimination of novel influenza A (H1N1) and influenza A and influenza B viruses using a single-tube multiplex RT-real time PCR.
Hong ZHANG ; Yong-Qiang HE ; Yan-Jun ZHANG ; Zhen WANG ; Zhen LI
Chinese Journal of Preventive Medicine 2012;46(3):273-276
OBJECTIVETo establish and evaluate a single-tube multiplex RT-real time PCR assay for detecting novel influenza A H1N1, influenza A and influenza B viruses (called "IV" for short) simultaneously.
METHODSA total of 213 clinical specimens of influenza-like patient's throat swab were collected during October 2010 and April 2011. 152 bp fragment in HA gene of novel influenza A H1N1 virus, 128 bp fragment in M gene of influenza A virus and 107 bp fragment in NP gene of influenza B virus were chosen as the target genes for multiplex RT-real time PCR, a specific primers and probes labeled with different fluoresceins were designed. The standard plasmid was constructed using in vitro transcription assay, and the standard curve was established. The reproducibility, specificity and sensitivity of the assay were evaluated. Furthermore, RNA extracted from 213 clinical specimens of throat swab was detected and verified by sequencing.
RESULTSThe corresponding standard curves of novel influenza A H1N1 virus, influenza A virus and influenza B virus were Y = - 3.46 lgX + 46.985, Y = - 3.49 lgX + 37.709, Y = - 3.51 lgX + 38.889, respectively; Y was cycle threshold (Ct), and lgX was logarithm value of virus replication number. The standard curve coefficient was 0.998. The detection limit of this assay was 10(2) copies/microl in one reaction. The specificity was strong. 39 (18.3%), 63 (29.6%) and 23 (10.8%) of 213 clinical specimens detected were positive for novel influenza A H1N1 virus RNA,influenza A virus RNA and influenza B virus RNA respectively. The positive samples were verified by sequencing.
CONCLUSIONThe single-tube multiplex RT-real time PCR assay developed in this study for detecting and identifying novel influenza A H1N1, influenza A and influenza B viruses simultaneously was rapid, specific and sensitive.
Humans ; Influenza A Virus, H1N1 Subtype ; genetics ; isolation & purification ; Influenza A virus ; genetics ; isolation & purification ; Influenza B virus ; genetics ; isolation & purification ; Reverse Transcriptase Polymerase Chain Reaction ; methods
8.Establishment of a method for rapid detection of the nucleic acid of the novel A (H1N1) influenza virus.
Da-Yan WANG ; Rong-Bao GAO ; Xiao-Dan LI ; Wei WANG ; Le-Ying WEN ; Shu-Mei ZOU ; Xiang ZHAO ; Xi-Yan LI ; Yu LAN ; Lei YANG ; Jun-Feng GUO ; Zi LI ; Yan-Hui CHENG ; Min-Jju TAN ; Xin-Wan LI ; Yu-Hong ZENG ; Yuan-Ji GUO ; De-Xin LI ; Yue-Long SHU
Chinese Journal of Virology 2009;25 Suppl():1-3
A new flu caused by a novel influenza A(H1N1) virus has spread over the United States, Mexico and more than 40 other countries. And because of the immediate global concern, WHO has announced that the current level of influenza pandemic alert is raised to phase 5, indicating approaching of an influenza pandemic. As patients suffering from the influenza A (H1N1) have the similar symptoms as patients with seasonal influenza, differential detection and identification of the influenza virus have to depend on specific laboratory tests. We have successfully developed a RT-PCR based method for detection of the influenza A (H1N1) virus, and had applied the method to detection of clinical samples.
Humans
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Influenza A Virus, H1N1 Subtype
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genetics
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isolation & purification
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Influenza, Human
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virology
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RNA, Viral
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genetics
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Reverse Transcriptase Polymerase Chain Reaction
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methods
9.Emerged Pdm09 influenza virus increased purifying selection of seasonal H1N1 influenza virus.
Yu LAN ; Wei-Juan HUANG ; Hong-Tao SUI ; Xi-Yan LI ; Xiang ZHAO ; Ming LI ; Yao-Yao CHEN ; Jun-Feng GUO ; Yan-Hui CHENG ; Min-Ju TAN ; Zhao WANG ; Ning XIAO ; He-Jiang WEI ; Da-Yan WANG ; Yue-Long SHU
Chinese Journal of Virology 2013;29(2):143-147
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
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Humans
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Influenza A Virus, H1N1 Subtype
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classification
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genetics
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isolation & purification
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Influenza, Human
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virology
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Phylogeny
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Seasons
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Selection, Genetic
10.Laboratory confirmation of the first influenza A (H1N1) imported case in Mainland China.
Wei WANG ; Ming PAN ; Guo-Hui CHANG ; Xiao-Dan LI ; Tian-Shu LI ; Cheng-Feng QIN ; Na JIA ; Le-Ying WEN ; Rong-Bao GAO ; Wen-Bin TONG ; Shu-Sen HE ; Da-Yan WANG ; Jun-Feng GUO ; Yu LAN ; Lei YANG ; Xiang ZHAO ; Xi-Yan LI ; Zi LI ; Shu-Mei ZOU ; Qing-Yu ZHU ; Yuan-Ji GUO ; Wu-Chun CAO ; De-Xin LI ; Yue-Long SHU
Chinese Journal of Virology 2009;25 Suppl():4-7
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
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Humans
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Influenza A Virus, H1N1 Subtype
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classification
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genetics
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isolation & purification
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Influenza, Human
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virology
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Molecular Sequence Data
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Phylogeny