Method used to identify previously undiagnosed infections in the HIV outbreak at Glenochil prison

Abstract

Four years after the occurrence of an outbreak of hepatitis B and HIV infection among injecting drug user inmates at Her Majesty's Prison Glenochil in Scotland, a study design was developed to complete the epidemiological account of the HIV outbreak. Our aim was to identify potential cases of (1) HIV transmission not diagnosed during the original outbreak investigation and (2) the source(s) of the outbreak. Scotland's HIV positive case register was searched for matches to a soundexed list of 636 Glenochil inmates imprisoned during January–June 1993. Eight HIV infections that may have been acquired in Glenochil and four possible sources of the outbreak were identified. The second stage of follow-up – molecular epidemiological techniques used on stored sera samples from identified individuals – is described in the companion paper. Without breach of medical or prisoner confidentiality, indirect and anonymous follow-up has proved possible for the Glenochil inmates.

A public health model for the molecular surveillance of HIV transmission in San Diego, California

“…In confirmatory phylogenetic analyses, amino acid residue sites associated with drug resistance[28] were stripped from all sequences to evaluate linkage independent of the presence of resistance associated mutations. If HIV transmission occurred between partners, then the genetic distance between the HIV isolates, should be so close as to not be likely to have occurred from a third party[29]. The sequence length necessary to detect and establish clustering was dependent on the average divergence between sequences from unrelated infections and the genetic distance between viral isolates obtained from closely related epidemiologically-linked partners (see results below)[29].…”

“…If HIV transmission occurred between partners, then the genetic distance between the HIV isolates, should be so close as to not be likely to have occurred from a third party[29]. The sequence length necessary to detect and establish clustering was dependent on the average divergence between sequences from unrelated infections and the genetic distance between viral isolates obtained from closely related epidemiologically-linked partners (see results below)[29]. Phylogenetic data were not disclosed to either partner and was used for participant recruitment in any cohort.…”

Long‐Term Persistence of Transmitted HIV Drug Resistance in Male Genital Tract Secretions: Implications for Secondary Transmission

“…For transmission to be confirmed through phylogenetic analysis, viral sequences from partner pairs should cluster together (share a most common recent ancestor) among the background of other possible sources of the infection sufficiently strongly that the association could not be due to chance and should be so similar relative to the other sequences as to reject the possibility that transmission occurred through a third party. The sequence length necessary to detect and establish linkage of infections is dependent on the information content, specifically the average divergence between strains from unrelated infections, which is ∼5% in conserved genes such as pol [16][17][18]. To ensure an unbiased assessment of linkage, background sequences from non-epidemiologically linked individuals who participated in the San Diego AIEDRP cohort were included in the phylogenetic analyses.…”

Molecular Epidemiology of Human Immunodeficiency Virus Type 1 Transmission in a Heterosexual Cohort of Discordant Couples in Zambia

“…However, a prerequisite for the acquisition of meaningful data, particularly with regard to predictors of contagion in the index seropositive partner, is the ability to confirm, with a high level of confidence, epidemiological linkage of HIV-1 transmission between members of all putative transmission pairs. Molecular analyses of suspected transmission links have been widely used to characterize localized HIV-1 outbreaks, mother-to-infant transmission, sexual transmission, sharing of contaminated needles, donation of contaminated blood, receipt of contaminated clotting reagent, nosocomial transmissions from health care workers, and intrafamilial contacts (1,4,5,6,13,18,21,29,36,42,44). In all of these cases, the establishment of epidemiological linkage relied on the documentation of closer genetic relatedness between viruses infecting the suspected transmission pair(s) compared to control viruses isolated from unrelated individuals in the same region.…”