Dataset Information

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses.

ABSTRACT:

Background

Phylogenetic analyses of HIV sequences are used to detect clusters and inform public health interventions. Conventional approaches summarize within-host HIV diversity with a single consensus sequence per host of the pol gene, obtained from Sanger or next-generation sequencing (NGS). There is growing recognition that this approach discards potentially important information about within-host sequence variation, which can impact phylogenetic inference. However, whether alternative summary methods that incorporate intra-host variation impact phylogenetic inference of transmission network features is unknown.

Methods

We introduce profile sampling, a method to incorporate within-host NGS sequence diversity into phylogenetic HIV cluster inference. We compare this approach to Sanger- and NGS-derived pol and near-whole-genome consensus sequences and evaluate its potential benefits in identifying molecular clusters among all newly-HIV-diagnosed individuals over six months at the largest HIV center in Rhode Island.

Results

Profile sampling cluster inference demonstrated that within-host viral diversity impacts phylogenetic inference across individuals, and that consensus sequence approaches can obscure both magnitude and effect of these impacts. Clustering differed between Sanger- and NGS-derived consensus and profile sampling sequences, and across gene regions.

Discussion

Profile sampling can incorporate within-host HIV diversity captured by NGS into phylogenetic analyses. This additional information can improve robustness of cluster detection.

SUBMITTER: Guang A

PROVIDER: S-EPMC8891961 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Publications

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses.

Guang August A Howison Mark M Ledingham Lauren L D'Antuono Matthew M Chan Philip A PA Lawrence Charles C Dunn Casey W CW Kantor Rami R

Frontiers in microbiology 20220217

<h4>Background</h4>Phylogenetic analyses of HIV sequences are used to detect clusters and inform public health interventions. Conventional approaches summarize within-host HIV diversity with a single consensus sequence per host of the <i>pol</i> gene, obtained from Sanger or next-generation sequencing (NGS). There is growing recognition that this approach discards potentially important information about within-host sequence variation, which can impact phylogenetic inference. However, whether alt ...[more]

PMID: 35250908

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Project description:BackgroundPeople with HIV infection in the United States are often affected by chronic viral hepatitis. These coinfected people with either HBV or HCV are at increased risk for serious, life-threatening complications. Coinfections with viral hepatitis may also complicate the delivery of anti-retroviral therapy (ART) by escalating the risk of drug-related hepatoxicity. According to the Centers for Disease Control and Prevention (CDC), approximately 10 percent of people with HIV in the United States also have HBV, and 25 percent also have HCV coinfection. With the advent of highly active antiretroviral therapy (HAART) and the increased life-expectancy of HIV patients, clinicians are more likely to be confronted with issues related to co-infection and the management challenges that they present, especially in resource-limited settings. The purpose of this analysis was to identify geographical clusters of HIV- (HBV/HCV) co-infection and compared to the geographical clusters of not co-infected using DC, Department of Health surveillance data. The results of the analysis will be used to target resources to areas at risk.MethodsHIV and Hepatitis surveillance data were matched among cases diagnosed between 1980 and 2016. HIV-hepatitis co-infected and the not co-infected spatial clusters were detected using discrete Poisson model. Kulldorff's spatial scan statistic method was implemented in the free software tool called SaTScan which has been widely adopted for detecting disease cluster. The analysis was conducted by tracts, but for visualization, ease of interpretation and assist in policy making the tract map was overlaid with the ward map using ArcGIS 10.5.1.ResultsBetween 1980 and 2016, there were 12,965 diagnosed cases of HIV, of which 2,316 HIV/Hepatitis matches were identified. Of the 2316 co-infected people living in DC, 25 percent (N = 590) of people had HBV, and 75 percent (N = 1,726) had HCV. Out of 12,965 diagnosed cases, remaining 10,649 did not have any co-infections (not co-infected). IDU (27.16 percent) and MSM (32.86 percent) were the highest mode of transmission for co-infected population. African-American were reported 83.64 percent (N = 1,937) among co-infection population. Three clusters were identified for both co-infected population in DC. The largest cluster radius for co-infected analysis covers wards 6, 7 and 8 as well as large parts of 2 and 5 (p < 0.001). Multiple clusters were identified for not co-infected population (p < 0.001). IDU (n = 450) was the highest mode of transmission for the co-infected clusters. For all clusters combined of not co-infected population highest mode of transmission were MSM (n = 2,534). This analysis also showed racial disparity, economic deprivation and lack of education were prominent in the co-infected clusters.ConclusionWe identified locations of high risk clusters where enhanced hepatitis and HIV prevention, treatment, and care can help combat the epidemic. The clusters radius expands into the neighboring state of Maryland as well. The findings from this analysis will be used to target area based public health policy and healthcare interventions for HIV-hepatitis. It is recommended based on the analysis that needle exchange programs can successfully control new HIV infections as well as hepatitis co-infections.

Dataset Information

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses.

Background

Methods

Results

Discussion

Publications

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses.

Similar Datasets

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