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

Javier E Cañada-García; Elena Delgado; Horacio Gil; Sonia Benito; Mónica Sánchez; Antonio Ocampo; Jorge Julio Cabrera; Celia Miralles; Elena García-Bodas; Ana Mariño; Patricia Ordóñez; María José Gude; Carmen Ezpeleta; Michael M Thomson

doi:10.3389/fmicb.2022.863084

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

Front Microbiol. 2022 May 27:13:863084. doi: 10.3389/fmicb.2022.863084. eCollection 2022.

Authors

Affiliations

¹ HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain.
² Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Spain.
³ Department of Microbiology, Complejo Hospitalario Universitario de Vigo, Vigo, Spain.
⁴ Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
⁵ Infectious Diseases Unit, Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain.
⁶ Department of Microbiology, Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain.
⁷ Department of Microbiology, Hospital Universitario Lucus Augusti, Lugo, Spain.
⁸ Department of Clinical Microbiology, Complejo Hospitalario de Navarra, Pamplona, Spain.

Abstract

Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Those derived from recombination between subtype B and subsubtype F1, with 18 reported, most of them of South American origin, are among the most diverse. In this study, we identified a HIV-1 BF1 recombinant cluster that is expanding in Spain, transmitted mainly via heterosexual contact, which, analyzed in near full-length genomes in four viruses, exhibited a coincident BF1 mosaic structure, with 12 breakpoints, that fully coincided with that of two viruses (10BR_MG003 and 10BR_MG005) from Brazil, previously classified as CRF72_BF1. The three remaining Brazilian viruses (10BR_MG002, 10BR_MG004, and 10BR_MG008) previously identified as CRF72_BF1 exhibited mosaic structures highly similar, but not identical, to that of the Spanish viruses and to 10BR_MG003 and 10BR_MG005, with discrepant subtypes in two short genome segments, located in pol and gp120^env. Based on these results, we propose that the five viruses from Brazil previously identified as CRF72_BF1 actually belong to two closely related CRFs, one comprising 10BR_MG002, 10BR_MG004, and 10BR_MG008, which keep their CRF72_BF1 designation, and the other, designated CRF122_BF1, comprising 10BR_MG003, 10BR_MG005, and the viruses of the identified Spanish cluster. Three other BF1 recombinant genomes, two from Brazil and one from Italy, previously identified as unique recombinant forms, were classified as CRF72_BF1. CRF122_BF1, but not CRF72_BF1, was associated with protease L89M substitution, which was reported to contribute to antiretroviral drug resistance. Phylodynamic analyses estimate the emergence of CRF122_BF1 in Brazil around 1987. Given their close phylogenetic relationship and similar structures, the grouping of CRF72_BF1 and CRF122_BF1 in a CRF family is proposed.

Keywords: HIV-1; circulating recombinant forms; molecular epidemiology; phylodynamics; phylogeny.