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Objective:To investigate the epidemiology, evolution and transmission characteristics of HIV-1 CRF07_BC in Nanjing between 2015 and 2019 to provide scientific basis for precise prevention and control of HIV-1 transmission.Methods:Pol gene sequences of 319 patients with HIV-1 CRF07_BC infection in Nanjing were amplified and sequenced and a maximum likelihood phylogenetic tree was then constructed. Markov Chain Monte Carlo sampling method was used to generate Maximum Clade Credibility Tree. Bayesian Skyline Plot was used to reconstruct the changing trend of the effective population size. Pairwise gene distance method was used to construct molecular network to investigate the transmission features. Results:Among the 319 patients, 303 (95.0%) were male; 264 (82.8%) had multiple sexual partners; only 14 (4.4%) had been using condoms. Most of the infections were occurred in men who have sex with men (MSM), accounting for 77.4%. The maximum likelihood phylogenetic analysis of HIV-1 CRF07_BC revealed two clusters: Cluster1 and Cluster2. Cluster1 mainly contained the strains isolated from MSM and Cluster2 mainly consisted of the strains isolated from heterosexual patients. The most recent common ancestor was 2002.47(1999.91, 2005.43) year for Cluster1 and 1996.38(1992.55, 1999.76) year for Cluster2. The evolutionary rates (95% highest posterior density, 95%HPD) of Cluster1 and Cluster2 were 1.73×10 -3 (1.36×10 -3-2.16×10 -3) substitutions·site -1·year -1 and 2.09×10 -3 (1.50×10 -3 -2.79×10 -3 ) substitutions·site -1·year -1, respectively. The effective population sizes of Cluster1 and Cluster2 tended to be stable after 2002 and 2003, respectively. In addition, Cluster1 and Cluster2 formed eleven and eight unique branches, respectively, suggesting the possibility of divergent epidemics of this genotype. A total of 35 propagation clusters were formed in the molecular propagation network, including 92 Nanjing sequences with an average degree of 4.3. Males, MSM and people with multiple sexual partners were more likely to be connected to the network. Students and young patients were more likely to be connected to the network. Conclusions:HIV-1 CRF07_BC infection was characterized by low age, multiple sexual partners, unprotected behaviors and transmission among MSM in Nanjing from 2015 to 2019. It was recommended to pay more attention to students and young people, to formulate more effective prevention and control measures for high-risk sexual behaviors, and to carry out continuous molecular monitoring of CRF07_BC strain, so as to provide scientific basis for the prevention and control of HIV CRF07_BC.
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Objectives@#The aims of this study were to analyze the characteristics of the 100 top-cited articles on scrub typhus (ST), and to assess the present research landscape and future research directions using bibliometric analysis. @*Methods@#Web of Science was used to conduct a bibliometric analysis of the 100 top-cited articles on ST. The articles were analyzed by publication year, number of citations, document type, journals, keywords, institutions, country of origin, and authorship. @*Results@#The top 100 articles on ST were published between 1945 to 2017. The number of citations ranges from 39 to 227 and the interquartile range was 35.5. The United States published the highest number ( n = 21) of articles. Mahidol University was the most prolific institution in terms of articles (n =14). The American Journal of Tropical Medicine and Hygiene was the journal with the most articles (n =14), and Paris DH was the most productive author in terms of the Hirsh-index, which was 10 for that author. The study revealed a significant correlation between the total number of citations and the number of authors (r=0.668, p < 0.001), number of institutions (r = 0.692, p < 0.001), number of years since publication (r=0.869, p <0.001), and number of countries involved (r=0.963, p <0.001). @*Conclusion@#The findings of this study provide landmarks in the publication and citationfrequency of the most influential articles on ST. In addition, this study provides useful information for readers and health policy-makers in evaluating the literature on ST.
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Objectives@#The aims of this study were to analyze the characteristics of the 100 top-cited articles on scrub typhus (ST), and to assess the present research landscape and future research directions using bibliometric analysis. @*Methods@#Web of Science was used to conduct a bibliometric analysis of the 100 top-cited articles on ST. The articles were analyzed by publication year, number of citations, document type, journals, keywords, institutions, country of origin, and authorship. @*Results@#The top 100 articles on ST were published between 1945 to 2017. The number of citations ranges from 39 to 227 and the interquartile range was 35.5. The United States published the highest number ( n = 21) of articles. Mahidol University was the most prolific institution in terms of articles (n =14). The American Journal of Tropical Medicine and Hygiene was the journal with the most articles (n =14), and Paris DH was the most productive author in terms of the Hirsh-index, which was 10 for that author. The study revealed a significant correlation between the total number of citations and the number of authors (r=0.668, p < 0.001), number of institutions (r = 0.692, p < 0.001), number of years since publication (r=0.869, p <0.001), and number of countries involved (r=0.963, p <0.001). @*Conclusion@#The findings of this study provide landmarks in the publication and citationfrequency of the most influential articles on ST. In addition, this study provides useful information for readers and health policy-makers in evaluating the literature on ST.
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Objective:To investigate HIV-1 genotypes and drug resistance among newly diagnosed young students in Nanjing in order to provide reference for the prevention and control of AIDS in this group.Methods:This study enrolled 200 newly diagnosed young students with HIV-1 infection in Nanjing from September 2015 to July 2019. Demographic information and blood samples were collected. Through RNA extraction and PCR amplification, 191 pol fragments were successfully obtained and subjected to genotyping and drug resistance analysis. Results:CRF01_AE (41.4%) and CRF07_BC (30.9%) were the predominant genotypes, followed by unique recombinant forms (URFs) (15.7%), CRF55_01B (5.2%), CRF68_01B (3.1%), CRF67_01B (2.6%), and subtype B (1.0 %). The incidence of drug-resistant mutations was 16.8%, and the rate of transmitted drug resistance (TDR) was 4.2%. The rates of TDR in CRF01_AE, CRF07_BC, CRF55_01B, URFs and other genotypes were 2.5%, 1.7%, 10.0%, 10.0% and 7.7%, respectively ( P>0.05). Conclusions:The rapid emergence of recombinant HIV-1 strains in the young students should be taken seriously. The prevalence of TDR was close to the alert level, thus needing to be monitored continuously.
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Objective To analyze the genetic characteristics and the evolution of the influenza A (H3N2) virus strains circulating in Jiangsu province between 2013 and 2014.Methods This study analyzed thirty-one representative strains of influenza A (H3N2) virus, which were isolated in different regions of Jiangsu province and during different time periods from 2013 to 2014.Results Genetic distances in nucleic acid and amino acid between a strain used for vaccine production (A/Texas/50/2012) and the 31 strains were 0.010 5 and 0.012 4.Similarities between them in nucleic acid and amino acid sequences were 97.9%-99.6% and 97.2%-99.3%.Phylogenetic analysis showed that the hemagglutinin (HA) genes of the 31 strains were divided into three different groups.Three strains isolated in 2013 and three strains isolated in 2014 belonged to Group 1 and Group 2, respectively, while the others belonged to Group 3.Three positive selection sites (237, 366 and 367) in HA protein were observed by REL model.Compared with the strain used for vaccine production, the 31 strains were characterized by amino acid substitutions (N128A/T and P198S/A) in HA protein and all of the mutations located in B-cell epitopes.The total number of mutation sites reached 24.Compared with the A/Texas/50/2012 strain, seven strains presented the glycosylation site 126NWT, and three strains showed disappeared glycosylation sites of 45NSS and 144NNS.Evaluation of vaccine efficacy for A(H3N2) virus strains showed that the vaccine efficacy was not very well.Conclusion The HA gene of A(H3N2) virus had undergone a greater variation and the vaccine efficacy was not very well in Jiangsu province during 2013 to 2014, which made the influenza A(H3N2) virus become the circulating strain.
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Objective To analyze the evolutionary characteristics and predict the variation trend of neuraminidase (NA) gene of influenza A/H1N1 (09pdm) virus in China from 2009 to 2016 in order to provide the basis of assessment for flu vaccines.Methods A total of 1 141 sequences of NA gene of influenza A/H1N1 (09pdm) virus were screened out from the Global Initiative on Sharing All Influenza Data and National Center for Biotechnology Information.The phylogenetic trees and the mutations of amino acids sequences were constructed and analyzed by biological softwares.The prediction for epidemic trend of influenza was analyzed by Bayesian skyline Plot.Results Compared with the sequence of reference strain,the homology of nucleic acid sequence of NA gene decreased year by year from 2009 to 2016.The phylogenetic analysis showed that NA gene clustered nearly on the identical phylogenetic tree in one year.The positive selection pressure site of NA strain was observed by different models in each year except 2012.The dynamics analysis showed that the popularity of influenza A/H1N1 virus may continue to increase to a peak in 2017.Conclusion The amino acid encoded by NA gene of influenza A/H1N1 virus is varying gradually,so the importance of surveillance for influenza virus should be reinforced for every year.
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Objective To understand the correlations between HIV-1 subtypes and changes in CD4+T cell count over time in patients with different subtypes of HIV-1 infection.Methods A total of 94 patients who were diagnosed with HIV-1 infection in Nanjing and received at least twice CD4+T cell counting test before antiretroviral therapy (ART) were recruited in this study.Descriptive analysis was used to present the rates of CD4+T cell decline for different HIV-1 subtypes.Logistic regression analysis and nonparametric test were conducted to investigate the factors responsible for CD4+T cell decline and to analyze the correlations between the rates of CD4+T cell decline and HIV-1 subtypes.Results The median monthly rate of CD4+T cell decline was-2.20 [interquartile range (IQR):-11.36-2.13] cell/μl.Of all patients,25.5% (24/94) had a significant decline (≥30%) in CD4+T cell count.Compared with the patients infected with CRF01_AE,those infected with CRF07_BC (OR=0.28,95%CI: 1.7-6.5) or other subtypes (OR=0.16,95%CI: 1.0-2.9) had a lower risk of significant decline in CD4+T cell count.In addition,results of the nonparametric test showed that the patients infected with CRF01_AE (M=-21.54,IQR:-30.97——11.92 cell/μl) had a faster CD4+T cell loss than those infected with CRF07_BC (M=-11.26,IQR:-14.06——5.63 cell/μl) (P=0.033).Conclusion HIV-1 subtype is associated with the rate of CD4+T cell decline.It is important to monitor the changes in CD4+T cell count in patients infected with CRF01_AE and to carry out timely ART.
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Objective@#To analyze the influence of growing experience on non-heterosexual orientation among male college students.@*Methods@#From October to November in 2015, a total of 2 535 male students from 96 classes in 14 colleges/departments were recruited from two colleges that participated in the experimental work of AIDS prevention by cluster random sampling method. A structured questionnaire was administered in this study, including general demographic information, growing experience and Kinsey scale (to evaluate sexual orientation). Out of 2 500 questionnaires distributed in this study, 2 332 effective copies were withdrew, with the effective rate at 93.3%. Chi square test was used to analyze the differences of non-heterosexual orientation among the individuals with different social demographic characteristics. Multivariate logistic regression model was used to analyze the influencing factors of non-heterosexual orientation.@*Results@#Among the 2 332 individuals, the proportion of self-reported non-heterosexual was 6.2% (144).The proportions of male students who identify as non-heterosexual from freshman to junior year were 5.2%(63/1216),6.9%(65/941),11.7%(13/111) and 4.7%(3/64), respectively (χ2=9.06,P=0.029). Compared with the individuals of very good relationship with parents, those with bad relationship (OR=3.3, 95%CI: 1.7-6.5) and general relationship (OR=1.7, 95%CI: 1.0-2.9) with parents had a higher risk of non-heterosexual orientation, respectively. Those encountered sexual assault had a higher risk of non-heterosexual orientation than those without encountered sexual assault (OR=5.9, 95%CI: 3.2-10.9).@*Conclusions@#This study reported a high proportion of self-reported non-heterosexual among college male students in Nanjing, and highlighted the importance of targeting students with poor parental relationships and who subjected to sexually abused.
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Objective To construct the molecular transmission networks of HIV-1 CRF01 AE strains circulating in China and to analyze their characteristics. Methods Sequences of the pol genes of Chinese CRF01 AE strains were downloaded from Los Alamos database and the related demographic informa-tion was checked. Transmission networks were created by four steps,including phylogenetic tree construc-tion,transmission cluster extraction,minimum genetic distance identification and network visualization. Chi-square test was performed to analyze the differences in the distribution of different populations in the networks and the differences in the distribution of subjects with different degrees among different sub-populations. De-scriptive analysis was used to investigate the transmission links between sub-populations and various regions. Results The 2 419 sequences constituted 250 separate networks including 847 nodes and 610 edges. The number of subjects covered by different networks ranged from 2 to 25. Subjects with degree ≥2 represented only 26. 4%(224 / 847)of network-individuals,but were connected with 66. 5%(563 / 847)of all network-individuals. There were 37. 6%(669 / 1 781)of men who have sex with men(MSM),28. 4%(102 / 359) of heterosexual men,16. 1%(10 / 62)of intravenous drug users(IDUs)and 30. 4%(66 / 217)of hetero-sexual women involved in the networks(χ2 =23. 774,P﹤0. 001). The percentage of subjects with degree ≥2 was high in MSM(10. 8% ,193 / 1 781)compared to that in heterosexual men(5. 6% ,20 / 359)(P =0. 002)and heterosexual women(4. 6% ,10 / 217)(P=0. 004). Of the 669 MSM in the networks,95. 5%(639 / 669)linked to other MSM and only 2. 4% (16 / 669)linked to heterosexual women. However, 15. 1%(10 / 66)of the heterosexual women in the networks linked to MSM. Of the heterosexual men in the networks,35. 3%(36 / 102)linked to heterosexual women,9. 8%(10 / 102)linked to MSM. Of the sub-jects in the networks,20. 9%(177 / 847)linked to other regions' individuals. Conclusion The super-spreaders played an important role in the molecular transmission networks of HIV-1 CRF01 AE strains even though they were in a minority. The transmission of HIV-1 CRF01 AE strains between sub-populations and various regions was complicated and active.
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Objective To analyze the substitutions at amino acid residues of neuraminidases ( NAs) in influenza B virus strains isolated in Jiangsu province from 2010 to 2012 and to further understand the genetic evolution of NAs in those influenza B virus strains .Methods Forty strains of influenza B virus isolated in Jiangsu province from 2010 to 2012 were screened out for this study .A two-step reverse transcrip-tion PCR ( RT-PCR) was performed to amply the gene fragments encoding the neuraminidases of influenza B virus strains.The PCR products were purified and then sequenced in an ABI 3730XL Genetic Analyzer.The evolutionary characteristics of NA gene were analyzed by using DNAStar , Bioedit, MEGA 5.0 and BEAST 1.8.0 softwares.Results The phylogenetic tree analysis of the NA genes showed that the NAs of 28 Vic-toria strains were derived from the Yamagata lineage .There were reassortments between the Victoria lineage-HA and theYamagata lineage-NA.Some of the strains added a glycosylation site at position 462.No substitu-tion was found in important enzyme active sites and neuraminidase inhibitor resistant sites .The Bayesian MCMC analysis showed that the estimated mean evolutionary rate for NA gene was 1.74×10-3(95%HPD:1.46×10-3-2.06×10-3) substitutions/site/year.The dN/dS ratio (ω), an indicator of selective pressure, was 0.24.Conclusion The important amino acid sites of NA were relatively conservative and the evolution -ary rate for NA gene was low .The dN/dS ratio was less than one , indicating that the NA gene was under pu-rifying selection .
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<p><b>BACKGROUND</b>PB1-F2 protein has been proven to increase the pathogenicity of influenza A virus (IAV) strains in primary infection and in secondary bacterial infection. It can also regulate the activity of viral polymerase. However, it was shown in another retrospective study that a portion of IAVs do not express full-length PB1-F2 protein during virus development; different kinds of stop codons cause exits in the open reading frames and form PB1-F2 gene products with the corresponding genotypes. Truncated PB1-F2 in human H3N2 IAVs has long been detected in North America but its evolution in China is still unclear.</p><p><b>METHODS</b>Influenza-like illnesses (ILIs) from the whole of Jiangsu Province were collected and inspected to determine the type and subtype of the viruses. A portion of isolates collected in the epidemic period were selected as samples for later whole-genome sequencing, and the exact sequences were determined and analyzed.</p><p><b>RESULTS</b>H3N2 influenza virus was one of the epidemical strains which had been prevalent during 2009-2010, in Jiangsu. Five H3N2 isolates with truncated PB1-F2 protein (25aa) were detected in influenza samples from Nanjing and Xuzhou, while seven similar H3N2 isolates were also reported in Niigata, Japan.</p><p><b>CONCLUSION</b>This emergence indicates the possibility that there has been transmission of the H3N2 virus between the two countries.</p>
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Humans , China , Epidemiology , Influenza A Virus, H3N2 Subtype , Genetics , Metabolism , Influenza, Human , Virology , Viral Proteins , Chemistry , Genetics , MetabolismABSTRACT
Objective To characterize the molecular characteristics of hemagglutinin (HA) and neuraminidase (NA) of influenza B viruses isolated in Jiangsu province,2011.Methods Thirteen strains of influenza B virus in different areas and epidemic period in Jiangsu province,2011 were selected for whole-genome sequencing,and analysis of molecule epidemic characteristics for HA and NA was carried out by bioinformatics method.Results Of the 13 randomly selected influeuza B strains,10 strains were assorted to Victoria lineage strains with NA genes from Yamagata lineage,and 3 strains belong to Yamagata lineage.Compared nucleotide and amino acid sequences of HA and NA genes with their vaccine strains respectiuely,196/197 glycosylation site appeared on HA1 gene in Yamagata/Victoria isolates virus.Conclusion Both B/Victoria and B/Yamagata lineage viruses co-circulated in Jiangsu province,and reassortant virus of Victoria lineage were predominant virus.