Transmission Clusters, Predominantly Associated With Men Who Have Sex With Men, Play a Main Role in the Propagation of HIV-1 in Northern Spain (2013–2018)

Abstract

Viruses of HIV-1-infected individuals whose transmission is related group phylogenetically in transmission clusters (TCs). The study of the phylogenetic relations of these viruses and the factors associated with these individuals is essential to analyze the HIV-1 epidemic. In this study, we examine the role of TCs in the epidemiology of HIV-1 infection in Galicia and the Basque County, two regions of northern Spain. A total of 1,158 HIV-1-infected patients from both regions with new diagnoses (NDs) in 2013–2018 were included in the study. Partial HIV-1 pol sequences were analyzed phylogenetically by approximately maximum-likelihood with FastTree 2. In this analysis, 10,687 additional sequences from samples from HIV-1-infected individuals collected in Spain in 1999–2019 were also included to assign TC membership and to determine TCs’ sizes. TCs were defined as those which included viruses from ≥4 individuals, at least 50% of them Spaniards, and with ≥0.95 Shimodaira-Hasegawa-like node support in the phylogenetic tree. Factors associated to TCs were evaluated using odds ratios (OR) and their 95% CI. Fifty-one percent of NDs grouped in 162 TCs. Male patients (OR: 2.6; 95% CI: 1.5–4.7) and men having sex with men (MSM; OR: 2.1; 95% CI: 1.4–3.2) had higher odds of belonging to a TC compared to female and heterosexual patients, respectively. Individuals from Latin America (OR: 0.3; 95% CI: 0.2–0.4), North Africa (OR: 0.4; 95% CI: 0.2–1.0), and especially Sub-Saharan Africa (OR: 0.02; 95% CI: 0.003–0.2) were inversely associated to belonging to TCs compared to native Spaniards. Our results show that TCs are important components of the HIV-1 epidemics in the two Spanish regions studied, where transmission between MSM is predominant. The majority of migrants were infected with viruses not belonging to TCs that expand in Spain. Molecular epidemiology is essential to identify local peculiarities of HIV-1 propagation. The early detection of TCs and prevention of their expansion, implementing effective control measures, could reduce HIV-1 infections.

Viruses Previously Identified in Brazil as Belonging to HIV-1 CRF72_BF1 Represent Two Closely Related Circulating Recombinant Forms, One of Which, Designated CRF122_BF1, Is Also Circulating in Spain

“…In a molecular epidemiological study in Spain, based on Pr-RT sequences, we detected frequent grouping in clusters, several of which were of F1 subsubtype in Pr-RT (Thomson et al, 2012;Delgado et al, 2015Delgado et al, , 2019Gil et al, 2022). One of them, designated F1_2, which is the focus of the present study, comprised 14 individuals, 13 of them from the region of Galicia, northwest Spain (Table 1).…”

The Origin, Epidemiology, and Phylodynamics of Human Immunodeficiency Virus Type 1 CRF47_BF

“…A similar phenomenon has been observed for the two other CRFs of South American origin identified by us in Spain: CRF66_BF ( Bacqué et al, 2021 ) and CRF89_BF ( Delgado et al, 2021 ). Such phenomenon may reflect the migration of these CRFs from countries where heterosexual transmission is predominant to Spain, where most currently expanding HIV-1 clusters are associated with MSM ( Patiño-Galindo et al, 2017 ; Gil et al, 2022 ). It should be pointed out, however, that outside of the Navarre cluster, the male:female ratio was 3.2:1, which contrasts to the 2.4:1 ratio of self-declared heterosexual men to MSM (decreasing to 1.5:1 if all men with non-specified sexual transmission were MSM).…”

Identification of a HIV-1 circulating BF1 recombinant form (CRF75_BF1) of Brazilian origin that also circulates in Southwestern Europe

“…In a HIV-1 molecular epidemiological study in Spain, based on analyses of Pr-RT sequences, we found frequent grouping of HIV-1 infections in clusters ( Gil et al, 2022 ), of which 25 were BF1 recombinant branching apart from reported CRF_BFs. One of these clusters, designated BF13 (numbered according to the order of identification), was further analyzed to determine whether it represents a new CRF.…”