{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,14]],"date-time":"2025-12-14T16:14:18Z","timestamp":1765728858015,"version":"build-2065373602"},"reference-count":48,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2022,12,25]],"date-time":"2022-12-25T00:00:00Z","timestamp":1671926400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases","award":["U01AI034994","KL2TR000102","KL2RR031974","P30AI117970"],"award-info":[{"award-number":["U01AI034994","KL2TR000102","KL2RR031974","P30AI117970"]}]},{"name":"National Center for Research Resources and the National Center for Advancing Translational Sciences","award":["U01AI034994","KL2TR000102","KL2RR031974","P30AI117970"],"award-info":[{"award-number":["U01AI034994","KL2TR000102","KL2RR031974","P30AI117970"]}]},{"name":"District of Columbia Center for AIDS Research, an NIH funded program","award":["U01AI034994","KL2TR000102","KL2RR031974","P30AI117970"],"award-info":[{"award-number":["U01AI034994","KL2TR000102","KL2RR031974","P30AI117970"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Background: Molecular epidemiological approaches provide opportunities to characterize HIV transmission dynamics. We analyzed HIV sequences and virus load (VL) results obtained during routine clinical care, and individual\u2019s zip-code location to determine utility of this approach. Methods: HIV-1 pol sequences aligned using ClustalW were subtyped using REGA. A maximum likelihood (ML) tree was generated using IQTree. Transmission clusters with \u22643% genetic distance (GD) and \u226590% bootstrap support were identified using ClusterPicker. We conducted Bayesian analysis using BEAST to confirm transmission clusters. The proportion of nucleotides with ambiguity \u22640.5% was considered indicative of early infection. Descriptive statistics were applied to characterize clusters and group comparisons were performed using chi-square or t-test. Results: Among 2775 adults with data from 2014\u20132015, 2589 (93%) had subtype B HIV-1, mean age was 44 years (SD 12.7), 66.4% were male, and 25% had nucleotide ambiguity \u22640.5. There were 456 individuals in 193 clusters: 149 dyads, 32 triads, and 12 groups with \u2265 four individuals per cluster. More commonly in clusters were males than females, 349 (76.5%) vs. 107 (23.5%), p &lt; 0.0001; younger individuals, 35.3 years (SD 12.1) vs. 44.7 (SD 12.3), p &lt; 0.0001; and those with early HIV-1 infection by nucleotide ambiguity, 202\/456 (44.3%) vs. 442\/2133 (20.7%), p &lt; 0.0001. Members of 43\/193 (22.3%) of clusters included individuals in different jurisdictions. Clusters \u2265 four individuals were similarly found using BEAST. HIV-1 viral load (VL) \u22653.0 log10 c\/mL was most common among individuals in clusters \u2265 four, 18\/21, (85.7%) compared to 137\/208 (65.8%) in clusters sized 2\u20133, and 927\/1169 (79.3%) who were not in a cluster (p &lt; 0.0001). Discussion: HIV sequence data obtained for HIV clinical management provide insights into regional transmission dynamics. Our findings demonstrate the additional utility of HIV-1 VL data in combination with phylogenetic inferences as an enhanced contact tracing tool to direct HIV treatment and prevention services. Trans-jurisdictional approaches are needed to optimize efforts to end the HIV epidemic.<\/jats:p>","DOI":"10.3390\/v15010068","type":"journal-article","created":{"date-parts":[[2022,12,27]],"date-time":"2022-12-27T07:30:06Z","timestamp":1672126206000},"page":"68","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States"],"prefix":"10.3390","volume":"15","author":[{"given":"Seble G.","family":"Kassaye","sequence":"first","affiliation":[{"name":"Department of Medicine, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zehava","family":"Grossman","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA"},{"name":"School of Public Health, Tel Aviv University, Tel Aviv 69978, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Priyanka","family":"Vengurlekar","sequence":"additional","affiliation":[{"name":"Department of Medicine, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William","family":"Chai","sequence":"additional","affiliation":[{"name":"Warren Alpert Medical School, Brown University, Providence, RI 02912, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Megan","family":"Wallace","sequence":"additional","affiliation":[{"name":"Department of Medicine, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1231-6542","authenticated-orcid":false,"given":"Soo-Yon","family":"Rhee","sequence":"additional","affiliation":[{"name":"Department of Medicine, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"III","given":"William A.","family":"Meyer","sequence":"additional","affiliation":[{"name":"Quest Diagnostics, Secaucus, NJ 07094, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harvey W.","family":"Kaufman","sequence":"additional","affiliation":[{"name":"Quest Diagnostics, Secaucus, NJ 07094, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amanda","family":"Castel","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, George Washington University, Washington, DC 20052, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeanne","family":"Jordan","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, George Washington University, Washington, DC 20052, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0836-3389","authenticated-orcid":false,"given":"Keith A.","family":"Crandall","sequence":"additional","affiliation":[{"name":"Computational Biology Institute, George Washington University, Ashburn, VA 20147, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alisa","family":"Kang","sequence":"additional","affiliation":[{"name":"Department of Medicine, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Princy","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Medicine, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David A.","family":"Katzenstein","sequence":"additional","affiliation":[{"name":"Department of Medicine, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2513-2643","authenticated-orcid":false,"given":"Robert W.","family":"Shafer","sequence":"additional","affiliation":[{"name":"Department of Medicine, Stanford University, Stanford, CA 94305, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frank","family":"Maldarelli","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1001\/jama.2019.1343","article-title":"Ending the HIV Epidemic: A Plan for the United States","volume":"321","author":"Fauci","year":"2019","journal-title":"JAMA"},{"key":"ref_2","unstructured":"Office of Infectious Disease and HIV\/AIDS Policy, HHS (2021, November 24). 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