Complex patterns of Hepatitis-C virus longitudinal clustering in a high-risk population

Rebecca Rose, Susanna L. Lamers, Guido Massaccesi, William Osburn, Stuart Campbell Ray, David L Thomas, Andrea Cox, Oliver B. Laeyendecker

Research output: Contribution to journalArticle

Abstract

We investigated longitudinal viral clustering among and within subjects in a highly networked cohort of people who inject drugs (PWID). All subjects had estimated dates of infection and two or more E1 sequences (bp 943–1288 relative to H77) with 1 to 14 years of follow up. Two methods (HIV-TRACE and PhyloPart) were used to determine clusters. Genetic distance thresholds were determined by comparing intra-and inter-host distances. Additional phylogenetic analysis was performed on subjects with complicated viral histories. At the optimal threshold of 3.9%, HIV-TRACE found 77 clusters and PhyloPart found 63 clusters, of which 27 and 32 contained multiple subjects, respectively. Furthermore, 1/3 of the subjects had sequences in different clusters over the course of the study, including some cases in which a later-sampled sequence matched a cluster detected much earlier in the infection, despite being separated by RNA-negative lab visit and detection of sequences in different clusters. A detailed phylogenetic analysis of four subjects with such patterns showed that in all four cases, the earlier and later variants grouped closely on the tree, and did not group with concurrent sequences from any other subject. These observations suggest that subjects are either experiencing rapid and recurring infection-clearance-reinfection cycles from the same source, or a single transmission event produces a chronic infection that may go undetected and/or co-circulate with different viruses from separate transmission events. Furthermore, our results show the utility of using longitudinal sampling to obtain a more comprehensive view of the viral linkages in high-risk populations.

Original languageEnglish (US)
Pages (from-to)77-82
Number of pages6
JournalInfection, Genetics and Evolution
Volume58
DOIs
StatePublished - Mar 1 2018

Fingerprint

hepatitis
Hepatitis C virus
Hepacivirus
Cluster Analysis
virus
human immunodeficiency virus
Infection
infection
Population
HIV
phylogenetics
phylogeny
genetic distance
linkage (genetics)
RNA
drug
Viruses
drugs
viruses
history

Keywords

  • Clustering
  • Epidemiology
  • HCV
  • Linkage
  • Phylogenetic

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Microbiology (medical)
  • Infectious Diseases

Cite this

Complex patterns of Hepatitis-C virus longitudinal clustering in a high-risk population. / Rose, Rebecca; Lamers, Susanna L.; Massaccesi, Guido; Osburn, William; Ray, Stuart Campbell; Thomas, David L; Cox, Andrea; Laeyendecker, Oliver B.

In: Infection, Genetics and Evolution, Vol. 58, 01.03.2018, p. 77-82.

Research output: Contribution to journalArticle

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