Next-Generation Sequencing Used to Characterize HIV Epidemic in Washington, DC

In 2018, Washington, DC, saw 340 newly diagnosed cases of HIV, according to a study published in Scientific Reports. The city’s rate is 5 times higher than the national rate, and it falls under the World Health Organization’s definition of an epidemic. Researchers used next-generation sequencing to gain a broader view of the disease’s dynamics in the DC area.

By using data from 68 participants enrolled in a longitudinal observational cohort study, funded by the National Institutes of Health, of people living with HIV-1 in Washington DC, researchers were able to determine specific phylodynamics of the disease. Blood samples were collected from participants between 2016 and 2017.

“Analyzing sequence data can detect new variants within the population, identify population structuring and associations with risk factors, and, in combination with demographic information, predict areas of interest to direct public health efforts,” the researchers said.

Drug resistant mutations (DRMs), subtypes, and HIV-1 diversity estimations were included in the results. The researchers found that men who have sex with men (MSM), heterosexual (HRH), and male participants in DC all exhibited higher HIV-1 diversity. In addition, 54% of participants in the study contained at least 1 DRM, and the highest levels of DRMs were found in those aged 40 to 49 (22.9%). In comparison, participants between ages 20 and 29 years did not have any DRMs.

To infer transmission clusters, haplotypes were reconstructed and “phylodynamic inferences based on the HIV-1 polymerase (pol) and envelope genes (env) were compared.” This analysis grouped 31.9% to 33.8% of participants in the study into clusters. By identifying transmission clusters, the researchers could, in the future, recognize groups that may be at risk of contracting HIV-1.

The majority of patients included in the trial were non-Hispanic black (82.4%) and male (69.1%). “The majority of participants were infected through heterosexual sexual contact (39.7%) followed closely by MSM sexual contact (35.3%).”

The researchers also found that participants infected through injection drug use had about half of the genetic diversity of MSM and HRH participants. High genetic diversity could be caused by risk groups intermingling and viral strains being exchanged among individuals.

“Our findings of a genetically diverse and complex HIV epidemic in DC are scientifically important,” said Keylie M. Gibson, a PhD student and lead author of the study, in a press release. “This study allowed us to give back to the District and the community through public health outreach and collaborations with organizations such as the DC Cohort.”

The study researchers recommend that future studies include more participants, specifically young adults and people with newly diagnosed HIV. Studies should also focus on the severity of transmitted drug resistance in the DC population, so as to enable effective intervention strategies targeting key populations.

Reference

Gibson KM, Jair K, Castel AD, et al; DC Cohort Executive Committee. A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. Sci Rep. 2020;10(1):1989. doi: 10.1038/s41598-020-58410-y.