目的对保定市新发现的1株pol区不能明确分型的HIV-1毒株(BD226AJ)进行近似全长基因组扩增,并分析其亚型、重组模式和基因特点。方法提取患者血浆中HIV-1RNA并逆转录为cDNA,使用近末端稀释法分2段对其进行近似全长基因组扩增并测序。使用...目的对保定市新发现的1株pol区不能明确分型的HIV-1毒株(BD226AJ)进行近似全长基因组扩增,并分析其亚型、重组模式和基因特点。方法提取患者血浆中HIV-1RNA并逆转录为cDNA,使用近末端稀释法分2段对其进行近似全长基因组扩增并测序。使用jpHMM和SimPlot 3.5软件对近似全长基因组序列进行重组模式和重组断点分析,采用MEGA 6.0软件分片段构建Neighbor-joining系统进化树进一步确认重组断点的准确性。构建该近似全长基因组序列及各亚型片段Neighbor-joining系统进化树,分析该毒株的亲本来源。结果经过近似全长基因组扩增、测序、序列拼接后,获得1条长度为8830 bp的HIV-1近似全长基因组序列。重组分析结果显示,该序列是由CRF01_AE和B亚型重组形成的,其近似全长基因组序列被3个断点分成了4个亚型片段,分别为ICRF01_AE(HXB2,823—4224 nt)、Ⅱ_(B)(HXB2,4225—5991 nt)、ⅢCRF01_AE(HX B2,5992—9295 nt)、ⅣB(HXB2,9296—9406 nt)。各亚型基因片段的系统进化树分析进一步表明该序列的可能亲本来源为CRF01_AE和B亚型。HIV BLAST的结果显示,该序列与CRF112_01B的相似性为96%,系统进化树分析进一步验证该序列与北京市男男性行为者(men who have sex with men,MSM)中的CRF112_01B序列聚集。结论本研究在保定市MSM人群中发现了1例由CRF01_AE和B亚型重组的新型重组毒株CRF112_01B,提示HIV-1CRF112_01B已通过MSM人群传入河北,并开始在保定市传播,因此加强该亚型或者类似新型毒株的监测,对有关部门采取针对性防控措施和遏制新型重组毒株在本地区的传播和流行具有重要意义。展开更多
Laos is the only landlocked country in Southeast Asia and borders Thailand,Myanmar and Cambodia,the three countries in this region that have been hardest hit by human immunodeficiency virus(HIV).Laos has been regarded...Laos is the only landlocked country in Southeast Asia and borders Thailand,Myanmar and Cambodia,the three countries in this region that have been hardest hit by human immunodeficiency virus(HIV).Laos has been regarded as a low-HIVprevalence country for decades.To understand the status of HIV in Laos in recent years,a retrospective study was performed among 2851 patients visiting a hospital in Vientiane,the capital of Laos,from November 2011 to May 2012.Whole blood samples were obtained from the patients,and DNA was extracted.HIV status was determined by HIV gag fragment-specific PCR assay.Sixty-nine samples were detected as HIV proviral DNA positive with a positive rate of 2.4%(69/2851).Sixty-one near full-length genomic sequences were obtained from the positive samples.The results of phylogenetic analysis showed that the vast majority(91.8%)of the HIV strains belonged to CRF01AE,and the other five(8.2%)strains were identified as a new HIV circulating recombinant form CRF9701B,which had a CRF01AE backbone with an insertion of subtype B in the gag-pol region.Phylogeographic analysis revealed that HIV CRF01AE circulating in Laos were multiply introduced from Thailand.These results indicated that Laos might be suffering a considerably more serious impact of HIV than previously believed.To keep this country from undergoing the same increase in HIV prevalence observed in its neighbors,immediate intervention measures and sufficient epidemiological research are urgently needed.展开更多
Background One of the major characteristics of the human immunodeficiency virus type 1 （HIV-1） is its unusually high degree of genetic variability, which involves in genetic diagnosis, subtyping, vaccine design, and...Background One of the major characteristics of the human immunodeficiency virus type 1 （HIV-1） is its unusually high degree of genetic variability, which involves in genetic diagnosis, subtyping, vaccine design, and epidemiology. HIV-1 CRF01_AE is a main prevalent HIV-1 recombinant strain in China. In this study, three full-length CRF01_AE genomes from Fujian Province, China were cloned, sequenced, and analyzed; and the further genetic diversity defining and epidemiologic analysis were carried out. Methods Proviral DNA was extracted from non-cultured peripheral blood mononuclear cells, the near full-length HIV-1 genome was amplified and the PCR products were cloned into pCR-XL-TOPO vector and sequenced. 5＇-long terminal repeat （LTR） and 3＇-LTRs were amplified by additional independent PCR and cloned into pMD18T vector. Gene-based phylogenic tree was constructed and genetic distances were calculated by MEGA 3.1. Simplot was used for Bootscan analysis. Results The phylogeny and genetic distance analysis of the three near full-length sequences confirmed that these three samples clustered with CRF01_AE isolates, more close to Thailand CRF01_AE strain CM240, and were distantly related to African CRF01_AE strain 90CF402. Analysis of their genomic organization revealed the presence of nine potential open reading frames. There were no major deletions, rearrangements, or insertions in the three sequences, but an in-frame stop codon was found in tat gene of Fj051. LTRs of the three sequences contained a few nucleotides mutation. We did not find new mosaic recombinant in the three sequences. The V3 motif was GPGQ in all the three sequences, and there were only few amino acids differences in all three V3 loop sequences. Conclusion This report reveals the background of the three full-length CRF01_AE genomes, the most dominantly circulating HIV-1 strain in Fujian Province, China. The work is essential for the design and development of an effective AIDS vaccine for the region.展开更多
文摘目的对保定市新发现的1株pol区不能明确分型的HIV-1毒株(BD226AJ)进行近似全长基因组扩增,并分析其亚型、重组模式和基因特点。方法提取患者血浆中HIV-1RNA并逆转录为cDNA,使用近末端稀释法分2段对其进行近似全长基因组扩增并测序。使用jpHMM和SimPlot 3.5软件对近似全长基因组序列进行重组模式和重组断点分析,采用MEGA 6.0软件分片段构建Neighbor-joining系统进化树进一步确认重组断点的准确性。构建该近似全长基因组序列及各亚型片段Neighbor-joining系统进化树,分析该毒株的亲本来源。结果经过近似全长基因组扩增、测序、序列拼接后,获得1条长度为8830 bp的HIV-1近似全长基因组序列。重组分析结果显示,该序列是由CRF01_AE和B亚型重组形成的,其近似全长基因组序列被3个断点分成了4个亚型片段,分别为ICRF01_AE(HXB2,823—4224 nt)、Ⅱ_(B)(HXB2,4225—5991 nt)、ⅢCRF01_AE(HX B2,5992—9295 nt)、ⅣB(HXB2,9296—9406 nt)。各亚型基因片段的系统进化树分析进一步表明该序列的可能亲本来源为CRF01_AE和B亚型。HIV BLAST的结果显示,该序列与CRF112_01B的相似性为96%,系统进化树分析进一步验证该序列与北京市男男性行为者(men who have sex with men,MSM)中的CRF112_01B序列聚集。结论本研究在保定市MSM人群中发现了1例由CRF01_AE和B亚型重组的新型重组毒株CRF112_01B,提示HIV-1CRF112_01B已通过MSM人群传入河北,并开始在保定市传播,因此加强该亚型或者类似新型毒株的监测,对有关部门采取针对性防控措施和遏制新型重组毒株在本地区的传播和流行具有重要意义。
基金supported in part by Grants from the National Natural Science Foundation of China(U1302224,81601802,81271892,81902106)
文摘Laos is the only landlocked country in Southeast Asia and borders Thailand,Myanmar and Cambodia,the three countries in this region that have been hardest hit by human immunodeficiency virus(HIV).Laos has been regarded as a low-HIVprevalence country for decades.To understand the status of HIV in Laos in recent years,a retrospective study was performed among 2851 patients visiting a hospital in Vientiane,the capital of Laos,from November 2011 to May 2012.Whole blood samples were obtained from the patients,and DNA was extracted.HIV status was determined by HIV gag fragment-specific PCR assay.Sixty-nine samples were detected as HIV proviral DNA positive with a positive rate of 2.4%(69/2851).Sixty-one near full-length genomic sequences were obtained from the positive samples.The results of phylogenetic analysis showed that the vast majority(91.8%)of the HIV strains belonged to CRF01AE,and the other five(8.2%)strains were identified as a new HIV circulating recombinant form CRF9701B,which had a CRF01AE backbone with an insertion of subtype B in the gag-pol region.Phylogeographic analysis revealed that HIV CRF01AE circulating in Laos were multiply introduced from Thailand.These results indicated that Laos might be suffering a considerably more serious impact of HIV than previously believed.To keep this country from undergoing the same increase in HIV prevalence observed in its neighbors,immediate intervention measures and sufficient epidemiological research are urgently needed.
基金This work was supported by a grant from the Fujian Scientific and Technological Research Program (No. 2004YZ01-2).
文摘Background One of the major characteristics of the human immunodeficiency virus type 1 （HIV-1） is its unusually high degree of genetic variability, which involves in genetic diagnosis, subtyping, vaccine design, and epidemiology. HIV-1 CRF01_AE is a main prevalent HIV-1 recombinant strain in China. In this study, three full-length CRF01_AE genomes from Fujian Province, China were cloned, sequenced, and analyzed; and the further genetic diversity defining and epidemiologic analysis were carried out. Methods Proviral DNA was extracted from non-cultured peripheral blood mononuclear cells, the near full-length HIV-1 genome was amplified and the PCR products were cloned into pCR-XL-TOPO vector and sequenced. 5＇-long terminal repeat （LTR） and 3＇-LTRs were amplified by additional independent PCR and cloned into pMD18T vector. Gene-based phylogenic tree was constructed and genetic distances were calculated by MEGA 3.1. Simplot was used for Bootscan analysis. Results The phylogeny and genetic distance analysis of the three near full-length sequences confirmed that these three samples clustered with CRF01_AE isolates, more close to Thailand CRF01_AE strain CM240, and were distantly related to African CRF01_AE strain 90CF402. Analysis of their genomic organization revealed the presence of nine potential open reading frames. There were no major deletions, rearrangements, or insertions in the three sequences, but an in-frame stop codon was found in tat gene of Fj051. LTRs of the three sequences contained a few nucleotides mutation. We did not find new mosaic recombinant in the three sequences. The V3 motif was GPGQ in all the three sequences, and there were only few amino acids differences in all three V3 loop sequences. Conclusion This report reveals the background of the three full-length CRF01_AE genomes, the most dominantly circulating HIV-1 strain in Fujian Province, China. The work is essential for the design and development of an effective AIDS vaccine for the region.
