Recent Increased Identification and Transmission of HIV-1 Unique Recombinant Forms in Sweden

Overview

Journal Sci Rep

Specialty Science

Date 2017 Jul 27

PMID 28744024

Citations 7

Authors

Ujjwal Neogi

Abu Bakar Siddik

Prabhav Kalaghatgi

Magnus Gisslen

Goran Bratt

Gaetano Marrone

Anders Sonnerborg

Affiliations

Soon will be listed here.

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.

Citing Articles

Information Theoretic Study of COVID-19 Genome.

Jacquet P Entropy (Basel). 2024; 26(3).

PMID: 38539735 PMC: 10968974. DOI: 10.3390/e26030223.

The molecular epidemiology of HIV-1 in Sweden 1996 to 2022, and the influence of migration from Ukraine.

Weibull Warnberg A, Brannstrom J, Elvstam O, Gisslen M, Mansson F, Sonnerborg A Euro Surveill. 2023; 28(48).

PMID: 38037731 PMC: 10690863. DOI: 10.2807/1560-7917.ES.2023.28.48.2300224.

Cohort profile: InfCareHIV, a prospective registry-based cohort study of people with diagnosed HIV in Sweden.

Carlander C, Brannstrom J, Mansson F, Elvstam O, Albinsson P, Blom S BMJ Open. 2023; 13(3):e069688.

PMID: 36931676 PMC: 10030896. DOI: 10.1136/bmjopen-2022-069688.

Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions.

Bennedbaek M, Zhukova A, Tang M, Bennet J, Munderi P, Ruxrungtham K Virus Evol. 2021; 7(2):veab055.

PMID: 34532059 PMC: 8438898. DOI: 10.1093/ve/veab055.

Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.

Gibson K, Steiner M, Rentia U, Bendall M, Perez-Losada M, Crandall K Viruses. 2020; 12(7).

PMID: 32674515 PMC: 7412389. DOI: 10.3390/v12070758.

References

Brannstrom J, Sonnerborg A, Svedhem V, Neogi U, Marrone G . A high rate of HIV-1 acquisition post immigration among migrants in Sweden determined by a CD4 T-cell decline trajectory model. HIV Med. 2017; 18(9):677-684. DOI: 10.1111/hiv.12509. View

Carr J, Salminen M, Albert J, Sanders-Buell E, Gotte D, Birx D . Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants. Virology. 1998; 247(1):22-31. DOI: 10.1006/viro.1998.9211. View

Hue S, Brown A, Ragonnet-Cronin M, Lycett S, Dunn D, Fearnhill E . Phylogenetic analyses reveal HIV-1 infections between men misclassified as heterosexual transmissions. AIDS. 2014; 28(13):1967-75. DOI: 10.1097/QAD.0000000000000383. View

Esbjornsson J, Mild M, Audelin A, Fonager J, Skar H, Bruun Jorgensen L . HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries. Virus Evol. 2016; 2(1):vew010. PMC: 4989887. DOI: 10.1093/ve/vew010. View

Siepel A, Halpern A, Macken C, Korber B . A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res Hum Retroviruses. 1995; 11(11):1413-6. DOI: 10.1089/aid.1995.11.1413. View

Sandstrom E, Uhnoo I, Ahlqvist-Rastad J, Bratt G, Berglund T, Gisslen M . Antiretroviral treatment of human immunodeficiency virus infection: Swedish recommendations. Scand J Infect Dis. 2003; 35(3):155-67. DOI: 10.1080/00365540310006395. View

Smyth R, Schlub T, Grimm A, Waugh C, Ellenberg P, Chopra A . Identifying recombination hot spots in the HIV-1 genome. J Virol. 2013; 88(5):2891-902. PMC: 3958072. DOI: 10.1128/JVI.03014-13. View

Carr J, Laukkanen T, Salminen M, Albert J, Alaeus A, Kim B . Characterization of subtype A HIV-1 from Africa by full genome sequencing. AIDS. 1999; 13(14):1819-26. DOI: 10.1097/00002030-199910010-00003. View

Gall A, Ferns B, Morris C, Watson S, Cotten M, Robinson M . Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes. J Clin Microbiol. 2012; 50(12):3838-44. PMC: 3502977. DOI: 10.1128/JCM.01516-12. View

10.

Laukkanen T, Albert J, Liitsola K, Green S, Carr J, Leitner T . Virtually full-length sequences of HIV type 1 subtype J reference strains. AIDS Res Hum Retroviruses. 1999; 15(3):293-7. DOI: 10.1089/088922299311475. View

11.

Martin D, Murrell B, Golden M, Khoosal A, Muhire B . RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evol. 2015; 1(1):vev003. PMC: 5014473. DOI: 10.1093/ve/vev003. View

12.

Antinori A, Coenen T, Costagiola D, Dedes N, Ellefson M, Gatell J . Late presentation of HIV infection: a consensus definition. HIV Med. 2010; 12(1):61-4. DOI: 10.1111/j.1468-1293.2010.00857.x. View

13.

Aralaguppe S, Siddik A, Manickam A, Ambikan A, Kumar M, Fernandes S . Multiplexed next-generation sequencing and de novo assembly to obtain near full-length HIV-1 genome from plasma virus. J Virol Methods. 2016; 236:98-104. DOI: 10.1016/j.jviromet.2016.07.010. View

14.

Amogne W, Bontell I, Grossmann S, Aderaye G, Lindquist L, Sonnerborg A . Phylogenetic Analysis of Ethiopian HIV-1 Subtype C Near Full-Length Genomes Reveals High Intrasubtype Diversity and a Strong Geographical Cluster. AIDS Res Hum Retroviruses. 2016; 32(5):471-4. DOI: 10.1089/aid.2015.0380. View

15.

Skar H, Sylvan S, Hansson H, Gustavsson O, Boman H, Albert J . Multiple HIV-1 introductions into the Swedish intravenous drug user population. Infect Genet Evol. 2008; 8(5):545-52. PMC: 2588350. DOI: 10.1016/j.meegid.2008.03.004. View

16.

Neogi U, Haggblom A, Santacatterina M, Bratt G, Gisslen M, Albert J . Temporal trends in the Swedish HIV-1 epidemic: increase in non-B subtypes and recombinant forms over three decades. PLoS One. 2014; 9(6):e99390. PMC: 4055746. DOI: 10.1371/journal.pone.0099390. View

17.

Philpott S, Burger H, Tsoukas C, Foley B, Anastos K, Kitchen C . Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood: compartmentalization and intrapatient recombination. J Virol. 2004; 79(1):353-63. PMC: 538688. DOI: 10.1128/JVI.79.1.353-363.2005. View

18.

Lole K, Bollinger R, Paranjape R, Gadkari D, Kulkarni S, Novak N . Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol. 1998; 73(1):152-60. PMC: 103818. DOI: 10.1128/JVI.73.1.152-160.1999. View

19.

Kalaghatgi P, Pfeifer N, Lengauer T . Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees. Mol Biol Evol. 2016; 33(10):2720-34. PMC: 5026249. DOI: 10.1093/molbev/msw123. View

20.

Struck D, Lawyer G, Ternes A, Schmit J, Perez Bercoff D . COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification. Nucleic Acids Res. 2014; 42(18):e144. PMC: 4191385. DOI: 10.1093/nar/gku739. View