Abstract
A temporal increase in non-B subtypes has earlier been described in Sweden by us and we hypothesized that this increased viral heterogeneity may become a hotspot for the development of more complex and unique recombinant forms (URFs) if the epidemics converge. In the present study, we performed subtyping using four automated tools and phylogenetic analysis by RAxML of pol gene sequences (n = 5246) and HIV-1 near full-length genome (HIV-NFLG) sequences (n = 104). A CD4+ T-cell decline trajectory algorithm was used to estimate time of HIV infection. Transmission clusters were identified using the family-joining method. The analysis of HIV-NFLG and pol gene described 10.6% (11/104) and 2.6% (137/5246) of the strains as URFs, respectively. An increasing trend of URFs was observed in recent years by both approaches (p = 0·0082; p < 0·0001). Transmission cluster analysis using the pol gene of all URFs identified 14 clusters with two to eight sequences. Larger transmission clusters of URFs (BF1 and 01B) were observed among MSM who mostly were sero-diagnosed in recent time. Understanding the increased appearance and transmission of URFs in recent years could have importance for public health interventions and the use of HIV-NFLG would provide better statistical support for such assessments.
Highlights
Description of regional epidemics of the human immunodeficiency virus type 1 (HIV-1) is facilitated by the large number of pol sequences generated for genotypic drug resistance testing (GRT) in clinical care
The appearance and spread of transmission clusters of unique recombinant forms (URFs) in Sweden over time was investigated using near full-length HIV-1 genomes (HIV-NFLG) and pol gene sequences
We identified an increased incidence of URFs among individuals diagnosed in the country and transmission of such strains within the country, in recent years
Summary
Description of regional epidemics of the human immunodeficiency virus type 1 (HIV-1) is facilitated by the large number of pol sequences generated for genotypic drug resistance testing (GRT) in clinical care. Using such sequences, we have earlier reported that all known subtypes and circulating recombinant forms (CRFs) are present in Sweden, to a large extent as a consequence of migration from high endemic African and Asian countries[1, 2]. Gene sequences obtained in clinical care from the national InfCare HIV database, which covers >99.9% of living patients, in order to give an overall picture of the appearance of URFs
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