Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States

Kassaye, Seble; Grossman, Zehava; Vengurlekar, Priyanka; Chai, William; Wallace, Megan A.; Rhee, Soo-Yon; Meyer, William A.; Kaufman, Harvey W.; Castel, Amanda D.; Jordan, Jeanne A.; Crandall, Keith A.; Kang, Alisa; Kumar, Princy; Katzenstein, David; Shafer, Robert W.; Maldarelli, Frank

doi:10.3390/v15010068

Cited by 3 publications

(1 citation statement)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, among HIV subtype B, we found evidence of strong HIV genetic similarity within small clusters of specific demographic groups. These results match recent analyses of sequencing data generated as part of routine clinical care in the mid-Atlantic region, where males, younger individuals, and those with recently acquired HIV, were more likely to represent clusters of infection [ 22 ]. All these findings are consistent with studies reporting that HIV diversity is associated with assortativity (selective mixing) within race/ethnicity groups and geography in the larger US population [ 23–25 ].…”

Section: Discussionsupporting

confidence: 85%

HIV Subtypes and Drug-resistance-associated Mutations in US Blood Donors, 2015–2020

Custer,

Altan,

Montalvo

et al. 2024

Open Forum Infectious Diseases

View full text Add to dashboard Cite

Background Monitoring genotypes of HIV infections in blood donors may provide insights into infection trends in the general population. Methods HIV RNA was extracted from plasma samples of blood donors confirmed as HIV-positive by blood screening nucleic acid and antibody tests. HIV genome target regions were amplified using nested real time-polymerase chain reaction followed by next generation sequencing. Sequences were compared to those in the Los Alamos National Laboratory (LANL) database. Sequences were also assessed for drug resistance mutations (DRM) using the Stanford HIV DRM Database. Results From available HIV-positive donations collected between September 1, 2015, and December 31, 2020, 563 of 743 (75.8%) were successfully sequenced; 4 were subtype A, 543 subtype B, 5 subtype C, 1 subtype G, 5 circulating recombinant forms (CRF), and 2 were subtype B and D recombinants. Overall, no significant differences between blood donor and available LANL genotypes were found, and the genotypes of newly acquired versus prevalent HIV infections in donors were similar. The proportion of non-B subtypes and CRF remained a small fraction, with no other subtype or CRF representing more than 1% of the total. DRM were identified in 122 (21.6%) samples with protease inhibitor, nucleoside reverse transcriptase inhibitor (NRTI) and non-NRTI DRMs identified in 4.9, 4.6 and 14.0% of samples, respectively. Conclusions HIV genetic diversity and DRM in blood donors appear representative of circulating HIV infections in the US general population and may provide more information on infection diversity than sequences reported to LANL, particularly for recently transmitted infections.

show abstract

Section: Discussionsupporting

confidence: 85%

HIV Subtypes and Drug-resistance-associated Mutations in US Blood Donors, 2015–2020

Custer,

Altan,

Montalvo

et al. 2024

Open Forum Infectious Diseases

View full text Add to dashboard Cite

show abstract

Unraveling distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes of Mycoplasma pneumoniae

You,

Yang,

Liu

et al. 2025

Emerging Microbes & Infections

View full text Add to dashboard Cite

High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA

Switzer,

Shankar,

Jia

et al. 2024

Virus Evolution

View full text Add to dashboard Cite

We investigated transmission dynamics of a large HIV outbreak among persons who inject drugs (PWID) in Kentucky and Ohio during 2017–2020 by using detailed phylogenetic, network, recombination, and cluster dating analyses. Using polymerase (pol) sequences from 193 people associated with the investigation, we document high HIV-1 diversity, including subtype B (44.6 per cent); numerous circulating recombinant forms (CRFs) including CRF02_AG (2.5 per cent) and CRF02_AG-like (21.8 per cent); and many unique recombinant forms (URFs) composed of CRFs with major subtypes and sub-subtypes (CRF02_AG/B (24.3 per cent), B/CRF02_AG/B (0.5 per cent), and A6/D/B (6.4 per cent)). Cluster analysis of sequences using a 1.5 per cent genetic distance identified 13 clusters, including a 75-member cluster composed of CRF02_AG-like and CRF02_AG/B, an 18-member CRF02_AG/B cluster, subtype B clusters of sizes ranging from two to 23, and a 9-member A6/D and A6/D/B cluster. Recombination and phylogenetic analyses identified CRF02_AG/B variants with 10 unique breakpoints likely originating from subtype B and CRF02_AG-like viruses in the largest clusters. The addition of contact tracing results from Ohio to the genetic networks identified linkage between persons with subtype B, CRF02_AG, and CRF02_AG/B sequences in the clusters supporting de novo recombinant generation. Superinfection prevalence was 13.3 per cent (8/60) in persons with multiple specimens and included infection with B and CRF02_AG; B and CRF02_AG/B; or B and A6/D/B. In addition to the presence of multiple, distinct molecular clusters associated with this outbreak, cluster dating inferred transmission associated with the largest molecular cluster occurred as early as 2006, with high transmission rates during 2017–2018 in certain other molecular clusters. This outbreak among PWID in Kentucky and Ohio was likely driven by rapid transmission of multiple HIV-1 variants including de novo viral recombinants from circulating viruses within the community. Our findings documenting the high HIV-1 transmission rate and clustering through partner services and molecular clusters emphasize the importance of leveraging multiple different data sources and analyses, including those from disease intervention specialist investigations, to better understand outbreak dynamics and interrupt HIV spread.

show abstract

Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States

Cited by 3 publications

References 41 publications

HIV Subtypes and Drug-resistance-associated Mutations in US Blood Donors, 2015–2020

HIV Subtypes and Drug-resistance-associated Mutations in US Blood Donors, 2015–2020

Unraveling distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes of Mycoplasma pneumoniae

High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA

Contact Info

Product

Resources

About