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      Molecular network analysis of 308 newly diagnosed HIV infection and 210 ART failure patients from rural counties in Sichuan

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          Abstract

          Background

          Few studies on molecular epidemiology have studied people with newly diagnosed HIV infection and ART Failure Patients at the same time in rural China. With more serious HIV epidemic than in other provinces in China, Sichuan is an area suitable for this study.

          Objective

          To analyze the characteristics of HIV-1 molecular networks and factors related to network entry among newly diagnosed HIV infection and ART Failure Patients in three county-level cities (A, B, C) in Sichuan Province, to provide scientific basis for accurate prevention and control.

          Methods

          Nested PCR amplification method was used to amplify HIV-1 pol gene region of 530 blood samples, Sequencer 4.9 was used to edit, clean and splice the gene sequence, Bioedit correction, Fastree 2.1.8 and Figtree 1.4.2 to construct evolutionary tree and determine genotype. HyPhy2.2.4 and Cytoscape 3.6.1 software were used to construct molecular network. Logistic regression analysis was applied.

          Results

          523(98.68%) pol sequences were obtained, and a total of 518 valid sequences with basic information came into the final analyses. A total of 6 genotypes were detected, namely CRF01_AE (320,61.78%), CRF07_BC (149,28.76%), B (30,5.79%), CRF08_BC (11, 2.12%), CRF55_01B (6, 1.16%) and C (2, 0.39%). 186 of 518(35.91%) sequences entered the network at a genetic distance of 0.8%, forming 42 propagation clusters. “High-risk transmitters”(connected with two and more) accounted for 21.62%. Logistic regression showed that≥50 years old (OR = 2.474) were more risky than 18–49 years old, CRF07_BC sub-type (OR = 0.174) were less risky than CRF01_AE sub-type, B sub-type (OR = 6.698) is higher risky than CRF01_AE sub-type, and District B (OR = 0.077) less risky than that of A city.

          Conclusion

          The sources of HIV infection in rural Sichuan are diversified and complicated. The prevention and control of HIV infection in Sichuan Province should focus on strengthening the long-term dynamic detection of elderly population, B strain sub-type, and in City A.

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          Most cited references36

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          Ending the HIV Epidemic

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            Biological network exploration with cytoscape 3.

            Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks composed of protein, gene, and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data, thereby facilitating research tasks such as predicting gene function and constructing pathways. Cytoscape provides core functionality to load, visualize, search, filter, and save networks, and hundreds of Apps extend this functionality to address specific research needs. The latest generation of Cytoscape (version 3.0 and later) has substantial improvements in function, user interface, and performance relative to previous versions. This protocol aims to jump-start new users with specific protocols for basic Cytoscape functions, such as installing Cytoscape and Cytoscape Apps, loading data, visualizing and navigating the networks, visualizing network associated data (attributes), and identifying clusters. It also highlights new features that benefit experienced users. Curr. Protoc. Bioinform. 47:8.13.1-8.13.24. © 2014 by John Wiley & Sons, Inc. Copyright © 2014 John Wiley & Sons, Inc.
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              Social and Genetic Networks of HIV-1 Transmission in New York City

              Background Sexually transmitted infections spread across contact networks. Partner elicitation and notification are commonly used public health tools to identify, notify, and offer testing to persons linked in these contact networks. For HIV-1, a rapidly evolving pathogen with low per-contact transmission rates, viral genetic sequences are an additional source of data that can be used to infer or refine transmission networks. Methods and Findings The New York City Department of Health and Mental Hygiene interviews individuals newly diagnosed with HIV and elicits names of sexual and injection drug using partners. By law, the Department of Health also receives HIV sequences when these individuals enter healthcare and their physicians order resistance testing. Our study used both HIV sequence and partner naming data from 1342 HIV-infected persons in New York City between 2006 and 2012 to infer and compare sexual/drug-use named partner and genetic transmission networks. Using these networks, we determined a range of genetic distance thresholds suitable for identifying potential transmission partners. In 48% of cases, named partners were infected with genetically closely related viruses, compatible with but not necessarily representing or implying, direct transmission. Partner pairs linked through the genetic similarity of their HIV sequences were also linked by naming in 53% of cases. Persons who reported high-risk heterosexual contact were more likely to name at least one partner with a genetically similar virus than those reporting their risk as injection drug use or men who have sex with men. Conclusions We analyzed an unprecedentedly large and detailed partner tracing and HIV sequence dataset and determined an empirically justified range of genetic distance thresholds for identifying potential transmission partners. We conclude that genetic linkage provides more reliable evidence for identifying potential transmission partners than partner naming, highlighting the importance and complementarity of both epidemiological and molecular genetic surveillance for characterizing regional HIV-1 epidemics.
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                Author and article information

                Contributors
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: SupervisionRole: VisualizationRole: Writing – original draft
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: SupervisionRole: VisualizationRole: Writing – original draft
                Role: Data curationRole: Investigation
                Role: Data curationRole: Investigation
                Role: Data curationRole: Investigation
                Role: Data curationRole: Investigation
                Role: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLOS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                16 February 2024
                2024
                : 19
                : 2
                : e0298324
                Affiliations
                [1 ] School of Management, Chengdu University of Traditional Chinese Medicine, Chengdu, China
                [2 ] Institute of HIV/AIDS prevention, Sichuan Center for Disease Control and Prevention, Chengdu, China
                [3 ] Department of HIV/AIDS prevention, Chengdu Center for Disease Control and Prevention, Chengdu, China
                Nanyang Technological University, SINGAPORE
                Author notes

                Competing Interests: The authors declare that they have no competing interests.

                Author information
                https://orcid.org/0000-0003-2825-4144
                Article
                PONE-D-22-09067
                10.1371/journal.pone.0298324
                10871515
                38363761
                df0aa4bb-83fd-4ef8-9ca9-038ddbcc08bf
                © 2024 Zhong et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 29 March 2022
                : 18 January 2024
                Page count
                Figures: 3, Tables: 3, Pages: 13
                Funding
                Funded by: National Natural Science Foundation of China Youth Fund Project
                Award ID: 81803300
                Award Recipient :
                This research was funded by the National Natural Science Foundation of China (81803300).
                Categories
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                Custom metadata
                This study contains sensitive patient information of 308 newly diagnosed HIV infection and 210 ART Failure Patients. According The Regulation on the Prevention and Treatment of HIV/AIDS of China, it is forbidden to disclose HIV/AIDS patient information in public. The datasets analyzed during the current study are available from the institutional review boards (IRB) Sichuan Center for Disease Prevention and Control on reasonable request (email: sccdcxqxpt@ 123456163.com ).

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