Host genetic variation at a locus near CHD1L impacts HIV sequence diversity in a South African population

Vanessa E Schulz; Jeffrey F Tuff; Riley H Tough; Lara Lewis; Benjamin Chimukangara; Nigel Garrett; Quarraisha Abdool Karim; Salim S Abdool Karim; Lyle R McKinnon; Ayesha B M Kharsany; Paul J McLaren

doi:10.1128/jvi.00954-23

Host genetic variation at a locus near CHD1L impacts HIV sequence diversity in a South African population

J Virol. 2023 Oct 31;97(10):e0095423. doi: 10.1128/jvi.00954-23. Epub 2023 Sep 25.

Authors

Vanessa E Schulz^{1

2}, Jeffrey F Tuff², Riley H Tough^{1

2}, Lara Lewis³, Benjamin Chimukangara^{3

4

5}, Nigel Garrett^{3

6}, Quarraisha Abdool Karim^{3

7}, Salim S Abdool Karim^{3

7}, Lyle R McKinnon^{1

3}, Ayesha B M Kharsany^{3

8}, Paul J McLaren^{1

2}

Affiliations

¹ Department of Medical Microbiology and Infectious Diseases, University of Manitoba , Winnipeg, Manitoba, Canada.
² Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada , Winnipeg, Manitoba, Canada.
³ Centre for the AIDS Programme of Research in South Africa , Durban, South Africa.
⁴ Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health , Bethesda, Maryland, USA.
⁵ Department of Virology, University of KwaZulu-Natal , Durban, South Africa.
⁶ Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal , Durban, South Africa.
⁷ Department of Epidemiology, Mailman School of Public Health, Columbia University , New York, New York, USA.
⁸ Department of Medical Microbiology, School of Laboratory Medicine and Medical Science, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa.

Abstract

It has been previously shown that genetic variants near CHD1L on chromosome 1 are associated with reduced HIV VL in African populations. However, the impact of these variants on viral diversity and how they restrict viral replication are unknown. We report on a regional association analysis in a South African population and show evidence of selective pressure by variants near CHD1L on HIV RT and gag. Our findings provide further insight into how genetic variability at this locus contributes to host control of HIV in a South African population.

Keywords: HIV; HLA; genome-to-genome analysis; host genomics; host-pathogen interaction; viral genomics; viral load.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

DNA Helicases* / genetics
DNA-Binding Proteins* / genetics
Genetic Loci*
Genetic Variation*
HIV Infections* / genetics
HIV Infections* / virology
HIV Reverse Transcriptase / metabolism
HIV-1* / genetics
Humans
South Africa
Viral Load / genetics
Virus Replication
gag Gene Products, Human Immunodeficiency Virus / metabolism

Substances

CHD1L protein, human
DNA Helicases
DNA-Binding Proteins
HIV Reverse Transcriptase
gag Gene Products, Human Immunodeficiency Virus

Abstract

Publication types

MeSH terms

Substances

Grants and funding