Transmission linking among networks, which is consistent with previous studies, suggesting that early HIV-1 infection has an important role in transmission events indeed19. This observation, once again, emphasizes the importance of early diagnosis and timely antiretroviral treatment. Previous studies showed that the individuals with more links in the network have a higher probability of spreading the virus to others because of a high viral load and a high rate of partner change20,21, and therefore, these individuals may play the role of super-spreaders22,23. Thus, our, genetic transmission network analysis confirmed that a minority of super-spreaders indeed drive transmission networks to a significant extend. An interesting observation in this study was that V179D/E, an NNRTI-associated mutation was dominating Shanghai MSM. Sequences with V179D/E were DM-3189MedChemExpress DM-3189 distributed and networked in most sub-lineages in SH-L1, suggesting that several independent CRF01_AE strains with V179D/E were involved in ongoing transmission in this city. Besides, we found a higher proportion of V179D/E mutation in Shanghai CRF01_AE strains than in all others China CRF01_AE strains. This observation constitutes an alternative molecular evidence for determination of HIV-1 transmission among Shanghai MSM. Although the present study was intended to include all first-time follow-up MSM after diagnosed, there was still 20 loss to follow. Besides a misclassification as heterosexuals could be present among MSM24. However, analysis of 50 subjects from the available follow-up subjects in this study was suggested to satisfy the requirements of cluster analysis in the concentrated areas25. Therefore, we believed that the size of samples derived from MSM was Doravirine biological activity reasonable and might not significantly bias our analysis. In conclusion, we elucidated the molecular evolutionary dynamics of HIV-1 CRF01_AE circulating among Shanghai MSM. Genetic transmission network analysis further revealed a complexity of transmission pattern. We thus suggest that network analysis based on a molecular approach, combined with social science and public health approaches could be helpful in effective HIV intervention strategy to curb the spread of virus and promote public health.DiscussionMethodssis during 01/2008-12/2013, representing >80 of newly HIV-1 diagnosed MSM in Shanghai. A total of 1, 836 sample sequences were acquired after RNA extraction and PCR amplification, among which, 1, 152 CRF01_AE isolate sequences with >1, 000 bp were selected for further analysis. The corresponding demographic characteristics and CD4 + T cell counts were also collected for analysis. None of the individuals was exposed to antiretroviral treatment (ART) at the time of enrolment. In addition, 130 heterosexual women sequences, 134 heterosexual men sequences and 18 PWID sequences were acquired from individuals diagnosed in Shanghai. We also isolated all closely related publicly available sequences with 1, 152 CRF01_AE strains of MSM from HIV databases ofScientific RepoRts | 6:34729 | DOI: 10.1038/srepStudy subjects. A total of 2, 252 MSM blood samples were collected at the first follow-up after HIV diagno-www.nature.com/scientificreports/Los Alamos National Laboratory. We performed a BLAST search26 by using the 1, 152 sequences, and selected top 10 sequences with the highest homology with the references for each sequence. A total of 795 reference sequences were selected for analysis after excluding repeated sequences. Ev.Transmission linking among networks, which is consistent with previous studies, suggesting that early HIV-1 infection has an important role in transmission events indeed19. This observation, once again, emphasizes the importance of early diagnosis and timely antiretroviral treatment. Previous studies showed that the individuals with more links in the network have a higher probability of spreading the virus to others because of a high viral load and a high rate of partner change20,21, and therefore, these individuals may play the role of super-spreaders22,23. Thus, our, genetic transmission network analysis confirmed that a minority of super-spreaders indeed drive transmission networks to a significant extend. An interesting observation in this study was that V179D/E, an NNRTI-associated mutation was dominating Shanghai MSM. Sequences with V179D/E were distributed and networked in most sub-lineages in SH-L1, suggesting that several independent CRF01_AE strains with V179D/E were involved in ongoing transmission in this city. Besides, we found a higher proportion of V179D/E mutation in Shanghai CRF01_AE strains than in all others China CRF01_AE strains. This observation constitutes an alternative molecular evidence for determination of HIV-1 transmission among Shanghai MSM. Although the present study was intended to include all first-time follow-up MSM after diagnosed, there was still 20 loss to follow. Besides a misclassification as heterosexuals could be present among MSM24. However, analysis of 50 subjects from the available follow-up subjects in this study was suggested to satisfy the requirements of cluster analysis in the concentrated areas25. Therefore, we believed that the size of samples derived from MSM was reasonable and might not significantly bias our analysis. In conclusion, we elucidated the molecular evolutionary dynamics of HIV-1 CRF01_AE circulating among Shanghai MSM. Genetic transmission network analysis further revealed a complexity of transmission pattern. We thus suggest that network analysis based on a molecular approach, combined with social science and public health approaches could be helpful in effective HIV intervention strategy to curb the spread of virus and promote public health.DiscussionMethodssis during 01/2008-12/2013, representing >80 of newly HIV-1 diagnosed MSM in Shanghai. A total of 1, 836 sample sequences were acquired after RNA extraction and PCR amplification, among which, 1, 152 CRF01_AE isolate sequences with >1, 000 bp were selected for further analysis. The corresponding demographic characteristics and CD4 + T cell counts were also collected for analysis. None of the individuals was exposed to antiretroviral treatment (ART) at the time of enrolment. In addition, 130 heterosexual women sequences, 134 heterosexual men sequences and 18 PWID sequences were acquired from individuals diagnosed in Shanghai. We also isolated all closely related publicly available sequences with 1, 152 CRF01_AE strains of MSM from HIV databases ofScientific RepoRts | 6:34729 | DOI: 10.1038/srepStudy subjects. A total of 2, 252 MSM blood samples were collected at the first follow-up after HIV diagno-www.nature.com/scientificreports/Los Alamos National Laboratory. We performed a BLAST search26 by using the 1, 152 sequences, and selected top 10 sequences with the highest homology with the references for each sequence. A total of 795 reference sequences were selected for analysis after excluding repeated sequences. Ev.
