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Genetic characterization of human immunodeficiency virus type 1 transmission in the Middle East and North Africa

Sallam, Malik LU ; Özkaya Sahin, Gülsen LU ; Ingman, Mikael LU ; Widell, Anders LU ; Esbjörnsson, Joakim LU and Medstrand, Patrik LU (2017) In Heliyon 3(7).
Abstract
Background: The HIV-1 spread in the Middle East and North Africa (MENA) has not been previously characterised using the phylogenetic approach. The aim of the current study was to investigate the genetic diversity and domestic transmission of HIV-1 in the MENA. Methods: A total of 2036 HIV-1 sequences available in Genbank and collected in the MENA during 1988–2016 were used together with 715 HIV-1 reference sequences that were retrieved from Genbank based on genetic similarity with the MENA sequences. The REGA and COMET tools were used to determine HIV-1 subtypes and circulating recombinant forms. Maximum Likelihood and Bayesian phylogenetic analyses were used to identify and date HIV-1 transmission clusters. Results:... (More)
Background: The HIV-1 spread in the Middle East and North Africa (MENA) has not been previously characterised using the phylogenetic approach. The aim of the current study was to investigate the genetic diversity and domestic transmission of HIV-1 in the MENA. Methods: A total of 2036 HIV-1 sequences available in Genbank and collected in the MENA during 1988–2016 were used together with 715 HIV-1 reference sequences that were retrieved from Genbank based on genetic similarity with the MENA sequences. The REGA and COMET tools were used to determine HIV-1 subtypes and circulating recombinant forms. Maximum Likelihood and Bayesian phylogenetic analyses were used to identify and date HIV-1 transmission clusters. Results: At least 21 HIV-1 subtypes and recombinant forms were prevalent in the MENA. Subtype B was the most common variant (39%), followed by CRF35_AD (19%) and CRF02_AG (14%). The most common genetic region was pol, and 675 partial pol sequences (average of 1005 bp) were eligible for detailed phylogenetic analysis. Fifty-four percent of the MENA sequences formed HIV-1 transmission clusters. Whereas numerous clusters were country-specific, some clusters indicated transmission links between countries for subtypes B, C and CRF02_AG. This was more common in North Africa compared with the Middle East (p < 0.001). Recombinant forms had a larger proportion of clustering compared to pure subtypes (p < 0.001). The largest MENA clusters dated back to 1991 (an Algerian CRF06_cpx cluster of 43 sequences) and 2002 (a Tunisian CRF02_AG cluster of 48 sequences). Conclusions: We found an extensive HIV-1 diversity in the MENA and a high proportion of sequences in transmission clusters. This study highlights the need for preventive measures in the MENA to limit HIV-1 spread in this region. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Health profession; Medicine; Infectious disease; Public health; Evolution; Genetics; Virology
in
Heliyon
volume
3
issue
7
pages
19 pages
publisher
Elsevier
external identifiers
  • scopus:85021997388
ISSN
2405-8440
DOI
10.1016/j.heliyon.2017.e00352
language
English
LU publication?
yes
id
9ddbd275-b112-45a7-9425-bb9e1db2738d
date added to LUP
2017-07-10 14:26:59
date last changed
2018-01-07 12:11:01
@article{9ddbd275-b112-45a7-9425-bb9e1db2738d,
  abstract     = {<b>Background:</b> The HIV-1 spread in the Middle East and North Africa (MENA) has not been previously characterised using the phylogenetic approach. The aim of the current study was to investigate the genetic diversity and domestic transmission of HIV-1 in the MENA. <b>Methods:</b> A total of 2036 HIV-1 sequences available in Genbank and collected in the MENA during 1988–2016 were used together with 715 HIV-1 reference sequences that were retrieved from Genbank based on genetic similarity with the MENA sequences. The REGA and COMET tools were used to determine HIV-1 subtypes and circulating recombinant forms. Maximum Likelihood and Bayesian phylogenetic analyses were used to identify and date HIV-1 transmission clusters. <b>Results:</b> At least 21 HIV-1 subtypes and recombinant forms were prevalent in the MENA. Subtype B was the most common variant (39%), followed by CRF35_AD (19%) and CRF02_AG (14%). The most common genetic region was pol, and 675 partial pol sequences (average of 1005 bp) were eligible for detailed phylogenetic analysis. Fifty-four percent of the MENA sequences formed HIV-1 transmission clusters. Whereas numerous clusters were country-specific, some clusters indicated transmission links between countries for subtypes B, C and CRF02_AG. This was more common in North Africa compared with the Middle East (p &lt; 0.001). Recombinant forms had a larger proportion of clustering compared to pure subtypes (p &lt; 0.001). The largest MENA clusters dated back to 1991 (an Algerian CRF06_cpx cluster of 43 sequences) and 2002 (a Tunisian CRF02_AG cluster of 48 sequences). <b>Conclusions: </b>We found an extensive HIV-1 diversity in the MENA and a high proportion of sequences in transmission clusters. This study highlights the need for preventive measures in the MENA to limit HIV-1 spread in this region.},
  articleno    = {e00352},
  author       = {Sallam, Malik and Özkaya Sahin, Gülsen and Ingman, Mikael and Widell, Anders and Esbjörnsson, Joakim and Medstrand, Patrik},
  issn         = {2405-8440},
  keyword      = {Health profession; Medicine; Infectious disease; Public health; Evolution; Genetics; Virology},
  language     = {eng},
  month        = {07},
  number       = {7},
  pages        = {19},
  publisher    = {Elsevier},
  series       = {Heliyon},
  title        = {Genetic characterization of human immunodeficiency virus type 1 transmission in the Middle East and North Africa},
  url          = {http://dx.doi.org/10.1016/j.heliyon.2017.e00352},
  volume       = {3},
  year         = {2017},
}