Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America

Elena Delgado,Lucı́a Pérez-Álvarez ,Josefa Muñoz ,Miren Z Zubero-Sulibarria,Ismael Fernández‐Miranda ,Mónica Sánchez ,Iciar Rodríguez-Avial ,Luis Elorduy,Horacio Gil,Marcos Pérez‐Losada ,Esther Culebras,Carmen Martín-Salas ,Silvia Hernáez ,María Luisa Giménez-Alarcón ,Ana Martínez-Sapiña ,María Moreno-Lorenzo ,Aurora Fernández-García ,Carmen Rodrı́guez ,Sonia Benito,María Maiques-Camarero ,J.j García-Irure ,Vanessa Montero,Gema Cenzual,Elena Bereciartúa ,Jorge Del Romero,Elena García-Bodas ,Carmen Gómez-González ,Michael M Thomson

doi:10.1038/s41598-021-90023-x

Abstract

Circulating recombinant forms (CRFs) contribute substantially to the HIV-1 pandemic. Among 105 CRFs described in the literature, 16 are BF intersubtype recombinants, most of South American origin, of which CRF12_BF is the most widely spread. A BF recombinant cluster identified in Bolivia was suggested to represent a new CRF_BF. Here we find that it belongs to a larger cluster incorporating 39 viruses collected in 7 countries from 3 continents, 22 of them in Spain, most from Bolivian or Peruvian individuals, and 12 in South America (Bolivia, Argentina, and Peru). This BF cluster comprises three major subclusters, two associated with Bolivian and one with Peruvian individuals. Near full-length genome sequence analyses of nine viruses, collected in Spain, Bolivia, and Peru, revealed coincident BF mosaic structures, with 13 breakpoints, 6 and 7 of which coincided with CRF12_BF and CRF17_BF, respectively. In a phylogenetic tree, they grouped in a clade closely related to these CRFs, and more distantly to CRF38_BF and CRF44_BF, all circulating in South America. These results allowed to identify a new HIV-1 CRF, designated CRF89_BF. Through phylodynamic analyses, CRF89_BF emergence was estimated in Bolivia around 1986. CRF89_BF is the fifth CRF member of the HIV-1 recombinant family related to CRF12_BF.

Highlights

One of the distinguishing features of HIV-1 evolution is its high recombination rate, which can be similar to or even greater than its mutation r ate[1,2]
In an HIV-1 molecular epidemiological study in Spain, we identified a phylogenetic cluster of 19 protease-reverse transcriptase (Pr-RT) sequences from samples collected in five regions, nested within the CRF12_BF clade
Epidemiological data from samples collected in Spain, available for all samples processed by us (Table 1) and from one database sequence, indicated that individuals in the BF cluster residing in Spain were predominantly male, of South American origin, and infected via heterosexual contact

Summary

Introduction

One of the distinguishing features of HIV-1 evolution is its high recombination rate, which can be similar to or even greater than its mutation r ate[1,2]. Recombinant forms are generated in individuals infected with two or more HIV-1 clades Those found in a single individual or a single epidemiologically-linked cluster are designated unique recombinant forms (URFs) and those found in three or more epidemiologically-unlinked individuals are designated circulating recombinant forms (CRFs)[15], of which 105 have been described in the literature. It has been proposed that all these recombinants constitute a “family”[31,32] of viruses that derive from a common recombinant ancestor, probably generated in Brazil from locally circulating B and F strains; subsequently, this ancestor would have gone through successive rounds of recombination with subtype B viruses, generating a great diversity of recombinant forms, some of which propagated epidemically, becoming CRFs29. We identify a fifth CRF member of the CRF12_BF-related family

Methods

Results

Conclusion