Molecular Characterization of Dengue Virus Serotype 2 Cosmospolitan Genotype From 2015 Dengue Outbreak in Yunnan, China
In 2015, a dengue outbreak with 1,067 reported cases occurred in Xishuangbanna, a city in China that borders Burma and Laos. To characterize the virus, the complete genome sequence was obtained and phylogenetic, mutation, substitution and recombinant analyses were performed. DENV-NS1 positive serum...
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Frontiers Media S.A.
2018-06-01
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| author | Liming Jiang Liming Jiang Liming Jiang Dehong Ma Chao Ye Chao Ye Chao Ye Chao Ye Lihua Li Xiaoman Li Jiajia Yang Jiajia Yang Jiajia Yang Yujiao Zhao Yujiao Zhao Yujiao Zhao Juemin Xi Juemin Xi Juemin Xi Xiaodan Wang Xiaodan Wang Xiaodan Wang Junying Chen Junying Chen Junying Chen Yue Pan Yue Pan Yue Pan Xiyun Shan Qiangming Sun Qiangming Sun Qiangming Sun |
| author_facet | Liming Jiang Liming Jiang Liming Jiang Dehong Ma Chao Ye Chao Ye Chao Ye Chao Ye Lihua Li Xiaoman Li Jiajia Yang Jiajia Yang Jiajia Yang Yujiao Zhao Yujiao Zhao Yujiao Zhao Juemin Xi Juemin Xi Juemin Xi Xiaodan Wang Xiaodan Wang Xiaodan Wang Junying Chen Junying Chen Junying Chen Yue Pan Yue Pan Yue Pan Xiyun Shan Qiangming Sun Qiangming Sun Qiangming Sun |
| author_sort | Liming Jiang |
| collection | DOAJ |
| description | In 2015, a dengue outbreak with 1,067 reported cases occurred in Xishuangbanna, a city in China that borders Burma and Laos. To characterize the virus, the complete genome sequence was obtained and phylogenetic, mutation, substitution and recombinant analyses were performed. DENV-NS1 positive serum samples were collected from dengue fever patients, and complete genome sequences were obtained through RT-qPCR from these serum samples. Phylogenetic trees were then constructed by maximum likelihood phylogeny test (MEGA7.0), followed by analysis of nucleotide mutation and amino acid substitution. The recombination events among DENVs were also analyzed by RDP4 package. The diversity analysis of secondary structure for translated viral proteins was also performed. The complete genome sequences of four amplified viruses (YNXJ10, YNXJ12, YNXJ13, and YNXJ16) were 10,742, 10,742, 10,741, and 10,734 nucleotides in length, and phylogenetic analysis classified the viruses as cosmopolitan genotype of DENV-2. All viruses were close to DENV Singapore 2013 (KX380828.1) and the DENV China 2013 (KF479233.1). In comparison to DENV-2SS (M29095), the total numbers of base substitutions were 712 nt (YNXJ10), 809 nt (YNXJ12), 772 nt (YNXJ13), and 841 nt (YNXJ16), resulting in 109, 171, 130, and 180 amino acid substitutions in translated regions, respectively. In addition, compared with KX380828.1, there were 44, 105, 64, and 116 amino acid substitutions in translated regions, respectively. The highest mutation rate occurred in the prM region, and the lowest mutation rate occurred in the NS4B region. Most of the recombination events occurred in the prM, E and NS2B/3 regions, which corresponded with the mutation frequency of the related portion. Secondary structure prediction within the 3,391 amino acids of DENV structural proteins showed there were 7 new possible nucleotide-binding sites and 6 lost sites compared to DENV-2SS. In addition, 41 distinct amino acid changes were found in the helix regions, although the distribution of the exposed and buried regions changed only slightly. Our findings may help to understand the intrinsic geographical relatedness of DENV-2 and contributes to the understanding of viral evolution and its impact on the epidemic potential and pathogenicity of DENV. |
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| spelling | doaj.art-d52a7985c9bf4d0593bdfd6aa626e4092022-12-22T00:44:59ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882018-06-01810.3389/fcimb.2018.00219345712Molecular Characterization of Dengue Virus Serotype 2 Cosmospolitan Genotype From 2015 Dengue Outbreak in Yunnan, ChinaLiming Jiang0Liming Jiang1Liming Jiang2Dehong Ma3Chao Ye4Chao Ye5Chao Ye6Chao Ye7Lihua Li8Xiaoman Li9Jiajia Yang10Jiajia Yang11Jiajia Yang12Yujiao Zhao13Yujiao Zhao14Yujiao Zhao15Juemin Xi16Juemin Xi17Juemin Xi18Xiaodan Wang19Xiaodan Wang20Xiaodan Wang21Junying Chen22Junying Chen23Junying Chen24Yue Pan25Yue Pan26Yue Pan27Xiyun Shan28Qiangming Sun29Qiangming Sun30Qiangming Sun31Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, ChinaYunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, ChinaYunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, ChinaXishuangbanna Dai Autonomous Prefecture People's Hospital, Xishuangbanna, ChinaInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, ChinaYunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, ChinaYunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, ChinaSchool of Basic Medicine, Kunming Medical University, Kunming, ChinaXishuangbanna Dai Autonomous Prefecture People's Hospital, Xishuangbanna, ChinaThe Affiliated Children's Hospital of Kunming Medical University, Kunming, ChinaInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, ChinaYunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, ChinaYunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, ChinaInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, ChinaYunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, ChinaYunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, ChinaInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, ChinaYunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, ChinaYunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, ChinaInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, ChinaYunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, ChinaYunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, ChinaInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, ChinaYunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, ChinaYunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, ChinaInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, ChinaYunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, ChinaYunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, ChinaXishuangbanna Dai Autonomous Prefecture People's Hospital, Xishuangbanna, ChinaInstitute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, ChinaYunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, ChinaYunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, ChinaIn 2015, a dengue outbreak with 1,067 reported cases occurred in Xishuangbanna, a city in China that borders Burma and Laos. To characterize the virus, the complete genome sequence was obtained and phylogenetic, mutation, substitution and recombinant analyses were performed. DENV-NS1 positive serum samples were collected from dengue fever patients, and complete genome sequences were obtained through RT-qPCR from these serum samples. Phylogenetic trees were then constructed by maximum likelihood phylogeny test (MEGA7.0), followed by analysis of nucleotide mutation and amino acid substitution. The recombination events among DENVs were also analyzed by RDP4 package. The diversity analysis of secondary structure for translated viral proteins was also performed. The complete genome sequences of four amplified viruses (YNXJ10, YNXJ12, YNXJ13, and YNXJ16) were 10,742, 10,742, 10,741, and 10,734 nucleotides in length, and phylogenetic analysis classified the viruses as cosmopolitan genotype of DENV-2. All viruses were close to DENV Singapore 2013 (KX380828.1) and the DENV China 2013 (KF479233.1). In comparison to DENV-2SS (M29095), the total numbers of base substitutions were 712 nt (YNXJ10), 809 nt (YNXJ12), 772 nt (YNXJ13), and 841 nt (YNXJ16), resulting in 109, 171, 130, and 180 amino acid substitutions in translated regions, respectively. In addition, compared with KX380828.1, there were 44, 105, 64, and 116 amino acid substitutions in translated regions, respectively. The highest mutation rate occurred in the prM region, and the lowest mutation rate occurred in the NS4B region. Most of the recombination events occurred in the prM, E and NS2B/3 regions, which corresponded with the mutation frequency of the related portion. Secondary structure prediction within the 3,391 amino acids of DENV structural proteins showed there were 7 new possible nucleotide-binding sites and 6 lost sites compared to DENV-2SS. In addition, 41 distinct amino acid changes were found in the helix regions, although the distribution of the exposed and buried regions changed only slightly. Our findings may help to understand the intrinsic geographical relatedness of DENV-2 and contributes to the understanding of viral evolution and its impact on the epidemic potential and pathogenicity of DENV.https://www.frontiersin.org/article/10.3389/fcimb.2018.00219/fulldengue virusgenomecharacterizationphylogenetic analysisrecombinant analysis |
| spellingShingle | Liming Jiang Liming Jiang Liming Jiang Dehong Ma Chao Ye Chao Ye Chao Ye Chao Ye Lihua Li Xiaoman Li Jiajia Yang Jiajia Yang Jiajia Yang Yujiao Zhao Yujiao Zhao Yujiao Zhao Juemin Xi Juemin Xi Juemin Xi Xiaodan Wang Xiaodan Wang Xiaodan Wang Junying Chen Junying Chen Junying Chen Yue Pan Yue Pan Yue Pan Xiyun Shan Qiangming Sun Qiangming Sun Qiangming Sun Molecular Characterization of Dengue Virus Serotype 2 Cosmospolitan Genotype From 2015 Dengue Outbreak in Yunnan, China Frontiers in Cellular and Infection Microbiology dengue virus genome characterization phylogenetic analysis recombinant analysis |
| title | Molecular Characterization of Dengue Virus Serotype 2 Cosmospolitan Genotype From 2015 Dengue Outbreak in Yunnan, China |
| title_full | Molecular Characterization of Dengue Virus Serotype 2 Cosmospolitan Genotype From 2015 Dengue Outbreak in Yunnan, China |
| title_fullStr | Molecular Characterization of Dengue Virus Serotype 2 Cosmospolitan Genotype From 2015 Dengue Outbreak in Yunnan, China |
| title_full_unstemmed | Molecular Characterization of Dengue Virus Serotype 2 Cosmospolitan Genotype From 2015 Dengue Outbreak in Yunnan, China |
| title_short | Molecular Characterization of Dengue Virus Serotype 2 Cosmospolitan Genotype From 2015 Dengue Outbreak in Yunnan, China |
| title_sort | molecular characterization of dengue virus serotype 2 cosmospolitan genotype from 2015 dengue outbreak in yunnan china |
| topic | dengue virus genome characterization phylogenetic analysis recombinant analysis |
| url | https://www.frontiersin.org/article/10.3389/fcimb.2018.00219/full |
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