Metagenomic Analysis of Environmental Samples from Wildlife Rescue Station at Poyang Lake, China / 生物医学与环境科学（英文）

OBJECTIVE@#To improve the understanding of the virome and bacterial microbiome in the wildlife rescue station of Poyang Lake, China.@*METHODS@#Ten smear samples were collected in March 2019. Metagenomic sequencing was performed to delineate bacterial and viral diversity. Taxonomic analysis was performed using the Kraken2 and Bracken methods. A maximum-likelihood tree was constructed based on the RNA-dependent RNA polymerase (RdRp) region of picornavirus.@*RESULTS@#We identified 363 bacterial and 6 viral families. A significant difference in microbial and viral abundance was found between samples S01-S09 and S10. In S01-S09, members of Flavobacteriia and Gammaproteobacteria were the most prevalent, while in S10, the most prevalent bacteria class was Actinomycetia. Among S01-S09, members of Myoviridae and Herelleviridae were the most prevalent, while the dominant virus family of S10 was Picornaviridae. The full genome of the pigeon mesivirus-like virus (NC-BM-233) was recovered from S10 and contained an open reading frame of 8,124 nt. It showed the best hit to the pigeon mesivirus 2 polyprotein, with 84.10% amino acid identity. Phylogenetic analysis showed that RdRp clustered into Megrivirus B.@*CONCLUSION@#This study provides an initial assessment of the bacteria and viruses in the cage-smeared samples, broadens our knowledge of viral and bacterial diversity, and is a way to discover potential pathogens in wild birds.

Galactomannan test combined with CD4+T lymphocytes for the diagnosis of invasive aspergillosis in patients with AIDS / 中国感染控制杂志

Objective To evaluate the effect of galactomannan(GM) test combined with CD4+ T lymphocyte detection on early diagnosis of invasive aspergillosis (IA) in patients with acquired immunodeficiency syndrome (AIDS).Methods 197 AIDS patients who were suspected with IA in a hospital from January 2014 to December 2016 were analyzed retrospectively,they were divided into confirmed IA group (n =35),clinically diagnosed IA group (n=96,suspected cases),and non-IA group(n =66),sensitivity and specificity of GM test and GM test combined CD4+ T lymphocyte counting for diagnosing IA were compared.Results In confirmed IA group,clinically diagnosed IA group,and non-IA group,the medium values of GM (minimum,maximum) were 1.29(0.65,1.84)pg /mL,0.91(0.36,1.23)pg /mL,and 0.11(0.28,0.72)pg /mL respectively,CD4+ T lymphocyte counting were 45 (29,69)cells/μL,79(35,99) cells/μL,and 89 (59,158) cells/μL respectively,GM value and CD4+ T lymphocyte counting among three groups were significantly different(all P＜0.05).The sensitivity and specificity of single GM test for diagnosing IA in AIDS patients were 64.9％ and 72.7％ respectively;sensitivity and specificity of two consecutive GM test within one week for diagnosing IA were 72.5 ％ and 95.5 ％ respectively;sensitivity and specificity of GM test combined CD4+ T lymphocyte counting were 86.3％ and 90.9％ respectively.Conclusion GM test has better diagnostic value for IA in AIDS patients,continuous GM test and GM test combined CD4+ T lymphocyte counting will further improve the clinical diagnostic value for IA.

Selection pressure analysis of H3N2 influenza virus from China between 1992 and 2012 / 中华实验和临床病毒学杂志

<p><b>OBJECTIVE</b>In order to investigate the relationship between selection pressure and the prevalence of antigenic clusters, we sequenced and analyzed the H3N2 influenza virus from China between 1992 and 2012.</p><p><b>METHODS</b>The H3N2 influenza virus (n = 1206) in China from 1992 to 2012 was analyzed, include global selection pressure and sites positive selection pressure analysis.</p><p><b>RESULTS</b>Considering all the H3N2 influenza viruses during these 21 years, a total of four amino acid sites subject to positive selection. The global selection pressure varies with the variation of different antigenic clusters and three years with peak bottom selection pressure were identified.</p><p><b>CONCLUSION</b>The global selection pressure rise from the peak bottom, a new antigenic clusters will appear andprevalent in the population, indicating the best time to replace the vaccine strain.</p>

Virological characterization of influenza A(H3N2) virus in Mainland China during 2011-2012 / 病毒学报

To study the prevalence and variation of influenza A(H3N2) viruses, the antigenic and genetic characteristics of influenza A(H3N2) viruses circulating in Mainland China during April 2011 to March 2012 were analyzed. The results showed that influenza A(H3N2) viruses increased gradually since 2012 and became the dominant strain since March. The viruses were antigenically closely related to the vaccine strain A/PER/16/09 (87.2%) and the representative virus A/FJ/196/09 (76.0%) in Mainland China. The genetic characteristics analysis results showed that recently isolated viruses belonged to the Vic/208 clade, and most of the low reaction strains also fell into the same clade. Crystal structure analysis of HA protein found that, compared with the vaccine strain A/PER/16/09, the recently isolated viruses had amino acid substitutions in the antigenic site A, B and C areas, in addition to gaining potential glycosylation sites at the amino acid position of 45 of HA and 367 of NA. Although the majority of circulating influenza A (H3N2) viruses in 2011-2012 season in Mainland China were antigeniclly matched by current influenza vaccine strain and the selected representative viruses, low reaction strains have increased since 2012, therefore it is necessary to strengthen the surveillance on the variation of influenza virus and to provide solid information for the vaccine strain selection.

Development of a real-time reverse transcriptase PCR assay for detection of E119V amino acid change in neuraminidase of influenza A (H3N2) using the TaqMan-MGB probe / 中华预防医学杂志

<p><b>OBJECTIVE</b>To develop a rapid duplex Real-time reverse transcription PCR (rRT-PCR) method to detect E119V mutation on neuraminidase (NA) of influenza A(H3N2) subtype with drug resistance to oseltamivir.</p><p><b>METHODS</b>Twenty-six NA genes of influenza A(H3N2) virus between 2000 and 2012 in GenBank database were selected as the target genes, and specific TaqMan-MGB probe was designed to target the E119V amino acid change in neuraminidase protein. rRT-PCR was then performed and evaluated for the sensitivity, specificity and reproducibility using virus with E119V mutation and clinical samples.</p><p><b>RESULTS</b>This study described the validation of a highly sensitive and specific duplex rRT-PCR for detection of substitutions leading to the E119V amino acid change in NA protein of influenza A(H3N2). Fluorescence signals could be detected even when diluted a A (H3N2) virus (HA = 8) into 10(-5) and linear correlation between the logarithm of the viral titer with the Ct values was observed. In addition, the assay was highly specific in that there was no cross-react with other respiratory viruses, nor did two TaqMan-MGB probes. E119V substitution in quasispecies with both sensitive and resistant viruses could be detected as well. The limit of detection was 5% for quasispecies with high concentrations and 50% for quasispecies with low concentrations. The average coefficient of variation (CV) for within-run assays was 2.32% and 0.57% for H3N2-119E and H3N2-119V primer/probe sets separately, 1.77% and 0.97% for average CV of between-run assays, which exhibited good repeatability. Sequence analysis of twenty NA genes verified glutamic acid (E) at amino acid site 119, which was in consistent with the results from our rRT-PCR method.</p><p><b>CONCLUSION</b>The assay developed in this study is highly sensitive and specific, and easy to operate; thereby it could be used for identification of A(H3N2) virus with E119V amino acid change in NA protein.</p>

Virological characterization of influenza B virus in mainland China during 2011-2012 / 病毒学报

In order to understand the prevalence and variation of influenza B viruses, the antigenic and genetic characteristics of influenza B viruses circulating in Mainland China during April, 2011 to March, 2012 were analyzed. The results showed the B Victoria lineage viruses were much more prevalent than B Yamagata lineage during this period, phylogenetic analysis showed vast majority of Victoria lineage viruses belong to genetic group 1, intra-clade reassortant between HA1 and NA gene was identified in a minor proportion of the viruses. 72.8% of the B/Victoria-lineage viruses were antigenically closely related to the vaccine strain B/Brisbane/60/2008. B Yamagata component was not included in the trivalent influenza vaccine in China during the study period, however vast majority of B Yamagata lineage viruses were antigenically and genetically closely related to the representative virus B/Hubei-Wujiagang/158/2009(97.8%) and B/Sichuan-Anyue/139/2011(85.2%) in China, reassortant between HA1 and NA was not identified in B Yamagata lineage viruses. Overall, the predominant circulating influenza B viruses in 2011-2012 season in China were matched by current influenza vaccine and the selected representative viruses were proved to represent the antigenic and genetic characteristics of the circulating viruses.

Emerged Pdm09 influenza virus increased purifying selection of seasonal H1N1 influenza virus / 病毒学报

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.

Analysis of genetic features of influenza B virus in Hunan province from 2007 to 2010 / 中华预防医学杂志

<p><b>OBJECTIVE</b>To investigate the gene variations of influenza B virus isolated in Hunan province from 2007 to 2010.</p><p><b>METHODS</b>A total of 42 strains of influenza B virus,which were isolated in the Influenza Surveillance Network Laboratories in Hunan province between year 2007 and 2010, were selected for the study. The hemagglutinin 1 (HA1) and neuraminidase (NA) genes of the selected strains were amplified by RT-PCR, and the sequence of the purified product were detected and homologically compared with the sequence of influenza vaccine strains isolated from Northern Hemisphere by WHO during the same period. In addition, the phylogenetic trees were constructed to characterize the molecular features.</p><p><b>RESULTS</b>In the Victoria branch of the HA1 gene phylogenetic tree, the strains isolated from year 2007 to 2009 were included in the V1 sub-branch, as well as the vaccine strain Malaysia/2506/2004; the strains isolated in year 2010 were involved in the V2 sub-branch, similar to the vaccine strains Brisbane/60/2008. In the Yamagata branch,the strains isolated in year 2007 were in the Y1 sub-branch,different from the strains isolated between year 2008 and 2010, which were in the Y2 sub-branch, instead. All virus in NA gene phylogenetic tree were included in the Yamagata branch, indicated their Yamagata origin. The genetic sequence analysis of the 7 strains isolated in year 2010 revealed that the viruses were classified as genotype 2 and genotype 15. The results of homological comparison between HA1 molecule and the influenza vaccine strains recommended by WHO were as below: Victoria lineage, 98.6% - 99.1% in 2007, 98.6% - 99.1% in 2008, 98.1% - 99.1% in 2009, and 97.6% - 99.1% in 2010; and Yamagata lineage, 97.9% - 98.5% in 2007, 97.9% - 98.5% in 2009 and 97.9% - 98.2% in 2010. The major mutations of the strains isolated in year 2007 were found in sites R48K, K88R, P108A, D197N and S230G. While the major mutations of the strains isolated between year 2009 and 2010 were sited in K88R, S150I, N166Y, D197N and S230G.</p><p><b>CONCLUSION</b>The prevalent influenza B virus isolated in Hunan province from 2007 to 2010 has mutated and evolved continuously.</p>

Establishment of a mouse-lethal model for pandemic H1N1 influenza virus / 病毒学报

To establish the mouse-lethal model for pandemic H1N1 influenza virus, provide an animal model for studying the pathogenicity and host adaptation of 2009 pandemic H1N1 influenza virus, and find out the key amino acid mutations which may affect viral virulence and replication. A pandemic H1N1 influenza virus strain, A/Sichuan/SWL1/2009 (H1N1, SC/1) was passaged in mouse lung by 15 cycles with intranasal infection. The passaged viruses were all propagated in MDCK cells and sequenced. Based on the sequencing results, four mice in each group were inoculated with 6 selected viruses and their weight and survival rate were monitored during the following 14 days after infection. Additionally, SC/1-MA P14 and P15 viruses were sequenced after purification by Plague Assay. Viral virulence was increased after serial passages and the mortality of 100% was detected after 7 passages. Several amino acid residue mutations of passaged viruses which may contribute to the enhanced virulence were observed. The increased virulence of passaged viruses and mammalian host adaptation maybe associated with amino acid mutations in viral functional proteins. Finally, we established a mouse-lethal model.

Colorimetric detection of human influenza A H1N1 virus by reverse transcription loop mediated isothermal amplification / 病毒学报

A simple, rapid and sensitive colorimetric Reverse Transcription Loop Mediated Isothermal Amplification (RT-LAMP) method was established to detect human influenza A H1N1 virus. The method employed a set of six specially designed primers that recognized eight distinct sequences of the HA gene for amplification of nucleic acid under isothermal conditions at 65 degrees C for one and half hour. The amplification process of RT-LAMP was monitored by the addition of HNB (Hydroxy naphthol blue) dye prior to amplification. A positive reaction was indicated by a color change from violet to sky blue and confirmed by agarose electrophoresis. The specificity of the RT-LAMP assay was validated by cross-reaction with different swine and human influenza virus including human seasonal influenza A /H1N1 A /H3N2, influenza B and swine A /H1N1. The sensitivity of this assay was evaluated by serial dilutions of RNA molecules from in vitro transcription of human influenza A H1N1 HA gene. The assay was further evaluated with 30 clinical specimens with suspected pandemic influenza A H1N1 virus infection in parallel with RT-PCR detection and 26 clinical specimens with seasonal influenza virus infection. Our results showed that the RT-LAMP was able to achieve a sensitivity of 60 RNA copies with high specificity, and detection rate was comparable to that of the RT-PCR with the clinical samples of pandemic influenza A H1N1 infection. The RT-LAMP reaction with HNB could also be measured at 650nm in a microplate reader for quantitative analysis. Thus, we concluded that this colorimetric RT-LAMP assay had potential for the rapid screening of the human influenza A H1N1 virus infection in National influenza monitoring network laboratories and sentinel hospitals of provincial and municipal region in China.

Study on the antigenicity and HA1 gene characteristics of influenza A viruses during 2004-2008 year in China / 中华实验和临床病毒学杂志

<p><b>OBJECTIVE</b>To under stand influenza A viruses epidemic, antigenicity and genetic characteristics variation between the vaccine and Circulation strains during 2004-2008 year in China.</p><p><b>METHODS</b>The influenza A viruses (H1N1, H3N2) isolated from 2004-2008 year were under took antigenic and sequence analysis. Influenza A virus antigenicity and genetic characteristics were analyzed thought amino acid variation compassion of HA1 protein of influenza A virus isolates.</p><p><b>RESULTS</b>The antigenicity of influenza H1N1 subtype viruses isolated from 2004 to 2007 is very similar with vaccine strain A/New Caledonia/20/1999 (HIN1)-like virus. The influenza H1N1 viruses circulated in 2008 year had similar antigenic characteristics with A/Brisben/59/2007 (H1N1) which is component of influenza vaccines for northern hemisphere 2008-2009 year. The influenza H3N2 subtype viruses of 2004-2005 year had antigenic variation comparatively with vaccine strain A/Fujian/411/12002 (H3N2), The antigenicity of 2006-2007 H3N2 viruses and 2008 year's is A/Wiscansin/67/2006(H3N2) and A/ Brisben/10/2006(H3N2) respectively.</p><p><b>CONCLUSION</b>There is change of influenza A viruses (H1N1, H3N2) antigenic and genetic characteristics during 2004-2008 in China.</p>

Establishment of a method for rapid detection of the nucleic acid of the novel A (H1N1) influenza virus / 病毒学报

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.

Laboratory confirmation of the first influenza A (H1N1) imported case in Mainland China / 病毒学报

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.