Exploring HIV-1 Transmission Dynamics by Combining Phylogenetic Analysis and Infection Timing

Abstract

HIV-1 pol sequences obtained through baseline drug resistance testing of patients newly diagnosed between 2013 and 2017 were analyzed for genetic similarity. For 927 patients the information on genetic similarity was combined with demographic data and with information on the recency of infection. Overall, 48.3% of the patients were genetically linked with 11.4% belonging to a pair and 36.9% involved in a cluster of ≥3 members. The percentage of early diagnosed (≤4 months after infection) was 28.6%. Patients of Belgian origin were more frequently involved in transmission clusters (49.7% compared to 15.3%) and diagnosed earlier (37.4% compared to 12.2%) than patients of Sub-Saharan African origin. Of the infections reported to be locally acquired, 69.5% were linked (14.1% paired and 55.4% in a cluster). Equal parts of early and late diagnosed individuals (59.9% and 52.4%, respectively) were involved in clusters. The identification of a genetically linked individual for the majority of locally infected patients suggests a high rate of diagnosis in this population. Diagnosis however is often delayed for >4 months after infection increasing the opportunities for onward transmission. Prevention of local infection should focus on earlier diagnosis and protection of the still uninfected members of sexual networks with human immunodeficiency virus (HIV)-infected members.

A Nationwide Study about the Dispersal Patterns of the Predominant HIV-1 Subtypes A1 and B in Greece: Inference of the Molecular Transmission Clusters

“…Our analysis suggested that regional transmission was associated for both subtypes with Greek origin, while the MSM risk group was identified as an additional associated parameter only for subtype A1 and more recent diagnosis and younger age for subtype B, respectively. These findings are in accordance with findings from Europe and the USA, where the MSM risk group, male gender, younger age, and recent diagnosis were the main factors associated with HIV-1 infections within MTCs [ 18 , 37 , 38 , 50 , 51 , 52 ], suggesting that prevention efforts should focus on populations with these characteristics. The exact effect of the time of sampling to MTCs cannot be estimated, since for sequences sampled earlier, identifying their transmission links is less likely and therefore, the likelihood is lower to be placed in MTCs [ 18 ].…”

“…We found that a high proportion of subtypes A1 and B, which are the predominant clades, occur locally at 93.8% and 77.0%, respectively. These provide some of the largest proportions of regional transmissions compared to approximately 50% that was reported previously [ 18 , 37 , 38 , 39 , 40 ]. Possible explanations are the dense sample used in our analysis (our study population represents the 57.2% of the total population of PLHIV diagnosed in Greece during 1999–2015) and the method implemented for the identification of MTCs that was based on phylogenetic analysis using a novel bootstrap approach, which is more appropriate for large datasets [ 29 ].…”

Use of HIV Recency Assays for HIV Incidence Estimation and Non-Incidence Surveillance Use Cases: A systematic review

“…Among non-incidence use cases, seven [91][92][93][94][95][96][97] described case-based surveillance among new HIV diagnoses in routine HIV programme settings and 2 described recency testing to inform targeted prevention planning, including one from a population-level cohort study 90 and one that described use of recency testing within three separate routine HIV country programs. 98 The quality of evidence was at least "moderately strong" in all 9/9 non-incidence use cases, each identified from the peer-reviewed literature.…”

“…90,92 In one example, researchers in Belgium analysed HIV-1 pol sequences obtained through baseline drug resistance testing of patients newly diagnosed with HIV between 2013 and 2017. 92 Information on genetic similarity was combined with demographic data and information on the recency of infection for 927 patients. They found that 48.3% of the patients were genetically linked to others, with 11.4% belonging to a pair and 36.9% involved in a cluster of Through TRACE, a lateral flow rapid recency assay is conducted as a supplementary test in routine HIV testing services and/or within HIV case surveillance to detect recent infection among newly diagnosed PLWH in all (or most) facility-and community-based testing sites in a country to drive prevention and care planning.…”

HIV Prevention Concepts—Counter Movements Challenging Societies

“…Insofar, it is noteworthy that in recent years, many comments have called for these OPH rules to be implemented in order to curb the ongoing spread of HIV and other STIs, which means a return to established rules.Most of the issues listed below have been selected from the references listedunder References, but are not cited here again.Preliminary remarks: We would like to note that only the combination of various measures related to specific situations may be helpful to reach the curb-ing of the HIV epidemic[111] [112][113]. There is also a complex need to adapt and implement current prevention campaigns to address the overlapping vulnerabilities of various at-risk key populations in modern societies[114] [115].Without a preventive vaccination, the vision "End of AIDS" remains questionable.1) HIV testing: People living unaware with their HIV infection present an unmanageable potential to keep upright, at least regional HIV epidemics; a multitude of benefits may result when reaching these people for testing for HIV and other STIs; this approach can help to reduce those who currently present with a late HIV diagnosis, late presenters[116]. The goal is to help them get treatment and link them to the respective healthcare services in the context of the TASP concept and medical service for acute and persistent health problems[117].…”