High prevalence and diversity of HIV-1 non-B genetic forms due to immigration in southern Spain: A phylogeographic approach

Abstract

Phylogenetic studies are a valuable tool to understand viral transmission patterns and the role of immigration in HIV-1 spread. We analyzed the spatio-temporal relationship of different HIV-1 non-B subtype variants over time using phylogenetic analysis techniques. We collected 693 pol (PR+RT) sequences that were sampled from 2005 to 2012 from naïve patients in different hospitals in southern Spain. We used REGA v3.0 to classify them into subtypes and recombinant forms, which were confirmed by phylogenetic analysis through maximum likelihood (ML) using RAxML. For the main HIV-1 non-B variants, publicly available, genetically similar sequences were sought using HIV-BLAST. The presence of HIV-1 lineages circulating in our study population was established using ML and Bayesian inference (BEAST v1.7.5) and transmission networks were identified. We detected 165 (23.4%) patients infected with HIV-1 non-B variants: 104 (63%) with recombinant viruses in pol: CRF02_AG (71, 43%), CRF14_BG (8, 4.8%), CRF06_cpx (5, 3%) and nine other recombinant forms (11, 6.7%) and unique recombinants (9, 5.5%). The rest (61, 37%) were infected with non-recombinant subtypes: A1 (30, 18.2%), C (7, [4.2%]), D (3, [1.8%]), F1 (9, 5.5%) and G (12, 7.3%). Most patients infected with HIV-1 non-B variants were men (63%, p < 0.001) aged over 35 (73.5%, p < 0.001), heterosexuals (92.2%, p < 0.001), from Africa (59.5%, p < 0.001) and living in the El Ejido area (62.4%, p<0.001). We found lineages of epidemiological relevance (mainly within Subtype A1), imported primarily through female sex workers from East Europe. We detected 11 transmission clusters of HIV-1 non-B Subtypes, which included patients born in Spain in half of them. We present the phylogenetic profiles of the HIV-1 non-B variants detected in southern Spain, and explore their putative geographical origins. Our data reveals a high HIV-1 genetic diversity likely due to the import of viral lineages that circulate in other countries. The highly immigrated El Ejido area acts as a gateway through which different subtypes are introduced into other regions, hence the importance of setting up epidemiological control measures to prevent future outbreaks.

HIV-1 Sub-Subtype A6: Settings for Normalised Identification and Molecular Epidemiology in the Southern Federal District, Russia

“…Subtype G strains are otherwise mostly reported from Nigeria and West African countries [27,28] (Table S8). They are rare in western countries, with the exceptions of Spain and Portugal, where they account for up to 12% and 30% of the infections, respectively [29][30][31][32]. In Russia, subtype G infections are unusual outside the region covered in this study [33].…”

Impact of HIV-1 subtypes on gross deletion in the nef gene after Korean Red Ginseng treatment

“…The high viral diversity of human immunodeficiency virus (HIV)-1 has possible implications for the differential rates of disease progression, responses to combination antiretroviral therapy (ART), and the development of a vaccine; however, there are confounders, such as access to medical care, nutritional status, socioeconomic level, host genetic factors, and mode of viral transmission [ [1] , [2] , [3] ]. HIV-1 subtype B is the most common subtype in developed countries, and accounts for approximately 11%–12% of the global epidemic [ 4 ]. Primary HIV-1 infections with various non-B subtypes (hereafter called non-B) are increasing in developed countries [ [4] , [5] , [6] ].…”

“…HIV-1 subtype B is the most common subtype in developed countries, and accounts for approximately 11%–12% of the global epidemic [ 4 ]. Primary HIV-1 infections with various non-B subtypes (hereafter called non-B) are increasing in developed countries [ [4] , [5] , [6] ]. There have been reports on the difference in disease progression among the patients infected with non-B [ [7] , [8] , [9] ].…”

Molecular Epidemiology of HIV-1 Subtype G in the Russian Federation

“…The most remarkable example is Portugal, where subtype G is the second most prevalent HIV-1 clade (>10%), after subtype B (>40%) [12,13,14]. In addition to Portugal, Spain has experienced an enormous spread of HIV; their epidemics are characterized by substantial viral diversity and distinct molecular properties compared to other European countries [15,16,17]. Non-B subtypes, particularly subtype G, were also very prevalent, with subtype G found in approximately 30% of all diagnoses [7].…”