Dynamics of Two Separate but Linked HIV-1 CRF01_AE Outbreaks among Injection Drug Users in Stockholm, Sweden, and Helsinki, Finland

Skar, Helena; Axelsson, Maria; Berggren, Ingela; Thalme, Anders; Gyllensten, Katarina; Liitsola, Kirsi; Brummer‐Korvenkontio, Henrikki; Kivelä, Pia; Spångberg, Erika; Leitner, Thomas; Albert, Jan

doi:10.1128/jvi.01413-10

Cited by 47 publications

(57 citation statements)

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“…However, the shorter branch lengths for MSM might also reflect a shorter time from infection to onward transmission for MSM compared to the comparison population. 7,44,45 Also, the subgroup of MSM might have been more densely sampled than the comparison population.…”

Section: Discussionmentioning

confidence: 99%

HIV Type 1 Transmission Networks Among Men Having Sex with Men and Heterosexuals in Kenya

Bezemer

Faria

Hassan

et al. 2014

AIDS Research and Human Retroviruses

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We performed a molecular phylogenetic study on HIV-1 polymerase sequences of men who have sex with men (MSM) and heterosexual patient samples in Kenya to characterize any observed HIV-1 transmission networks. HIV-1 polymerase sequences were obtained from samples in Nairobi and coastal Kenya from 84 MSM, 226 other men, and 364 women from 2005 to 2010. Using Bayesian phylogenetics, we tested whether sequences clustered by sexual orientation and geographic location. In addition, we used trait diffusion analyses to identify significant epidemiological links and to quantify the number of transmissions between risk groups. Finally, we compared 84 MSM sequences with all HIV-1 sequences available online at GenBank. Significant clustering of sequences from MSM at both coastal Kenya and Nairobi was found, with evidence of HIV-1 transmission between both locations. Although a transmission pair between a coastal MSM and woman was confirmed, no significant HIV-1 transmission was evident between MSM and the comparison population for the predominant subtype A (60%). However, a weak but significant link was evident when studying all subtypes together. GenBank comparison did not reveal other important transmission links. Our data suggest infrequent intermingling of MSM and heterosexual HIV-1 epidemics in Kenya.

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Section: Discussionmentioning

confidence: 99%

HIV Type 1 Transmission Networks Among Men Having Sex with Men and Heterosexuals in Kenya

Bezemer

Faria

Hassan

et al. 2014

AIDS Research and Human Retroviruses

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“…However, the interpretation of phylogenetic trees has broader importance beyond criminal investigations. Phylogenetics now plays an increasingly central role in public health investigations and practices (20)(21)(22)(23)(24).…”

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confidence: 99%

Phylogenetically resolving epidemiologic linkage

Romero-Severson

Bulla

Leitner

2016

Proc. Natl. Acad. Sci. U.S.A.

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134

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Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals' HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.HIV-1 | transmission | paraphyly | coalescent | phylogeny

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“…However, in various countries with large immigrant communities, the epidemiology of HIV-1 infection has evolved over the past decade toward a marked increase in the circulation of non-B strains (1,17,26,29). The recent report of HIV-1 CRF01_AE outbreaks among injection drug users in Sweden and Finland demonstrated that standing social networks with risky behavior can contribute to the spread of HIV-1 subtypes otherwise barely detected in Western Europe (27). In France, HIV transmission disproportionately affects certain risk groups and seems to be out of control in the population of men having sex with men (MSM), who make up 48% of all new infections and have a persistently high incidence of 1% per year (16).…”

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confidence: 99%

Continuous Spread of HIV-1 Subtypes D and CRF01_AE in France from 2003 to 2009

et al. 2012

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Among 61 and 35 patients who were infected in France by viruses of the rare clades D and CRF01_AE, respectively, approximately half of them originated from areas where HIV-1 is endemic, but the data showed that both clades have spread in the French indigenous population, particularly in men having sex with men (MSM). One of the characteristics of the human immunodeficiency virus type 1 (HIV-1) pandemic is the tremendous genetic heterogeneity of the virus, leading to the identification of many subepidemics due to specific variants. Group M viruses, the pandemic branch of HIV-1, can be subdivided into phylogenetic subtypes (named A to D, F to H, J, and K), sub-subtypes (A1 and A2, F1 and F2), and circulating recombinant forms (CRFs). The most prevalent HIV-1 genetic forms worldwide are subtypes A, B, and C (7, 12). However, there is a specific geographic distribution pattern for HIV-1 subtypes, and less prevalent genetic forms can reach high proportions locally (2,9,12,18,20,24). The relevance of CRFs in the global HIV-1 pandemic has also become clear, and particular CRFs are the predominant forms in Southeast Asia (CRF01_AE) and in West Africa (CRF02_AG) (12,23).Subtype B is the most prevalent genetic form in Western Europe. However, in various countries with large immigrant communities, the epidemiology of HIV-1 infection has evolved over the past decade toward a marked increase in the circulation of non-B strains (1,17,26,29). The recent report of HIV-1 CRF01_AE outbreaks among injection drug users in Sweden and Finland demonstrated that standing social networks with risky behavior can contribute to the spread of HIV-1 subtypes otherwise barely detected in Western Europe (27). In France, HIV transmission disproportionately affects certain risk groups and seems to be out of control in the population of men having sex with men (MSM), who make up 48% of all new infections and have a persistently high incidence of 1% per year (16).To assess the circulation of rare HIV-1 subtypes in France, we studied the epidemiological characteristics of patients infected with HIV-1 subtype D and CRF01_AE identified through the national HIV cases surveillance program from January 2003 to December 2009. We decided to focus on HIV-1 group M clades D and CRF01_AE for various reasons. First, these two genetic forms have different epidemiological characteristics. The HIV-1 subtype D prevalence in Africa is slowly decaying, and its introduction in

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Dynamics of Two Separate but Linked HIV-1 CRF01_AE Outbreaks among Injection Drug Users in Stockholm, Sweden, and Helsinki, Finland

Cited by 47 publications

References 35 publications

HIV Type 1 Transmission Networks Among Men Having Sex with Men and Heterosexuals in Kenya

HIV Type 1 Transmission Networks Among Men Having Sex with Men and Heterosexuals in Kenya

Phylogenetically resolving epidemiologic linkage

Continuous Spread of HIV-1 Subtypes D and CRF01_AE in France from 2003 to 2009

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