Estimating the in-vivo HIV template switching and recombination rate

Cromer, Deborah, Grimm, Andrew J., Schlub, Timothy E., Mak, Johnson and Davenport, Miles P. 2016, Estimating the in-vivo HIV template switching and recombination rate, AIDS : official journal of the international AIDS society, vol. 30, no. 2, pp. 185-192, doi: 10.1097/QAD.0000000000000936.

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Title Estimating the in-vivo HIV template switching and recombination rate
Author(s) Cromer, Deborah
Grimm, Andrew J.
Schlub, Timothy E.
Mak, JohnsonORCID iD for Mak, Johnson orcid.org/0000-0002-5229-5707
Davenport, Miles P.
Journal name AIDS : official journal of the international AIDS society
Volume number 30
Issue number 2
Start page 185
End page 192
Total pages 8
Publisher Lippincott Williams & Wilkins
Place of publication Philadelphia, Pa.
Publication date 2016
ISSN 1473-5571
Keyword(s) Science & Technology
Life Sciences & Biomedicine
Immunology
Infectious Diseases
Virology
HIV
HIV evolution
in vivo
mathematical modelling
recombination rate
reverse transcription
template switching
IMMUNODEFICIENCY-VIRUS TYPE-1
GENETIC-RECOMBINATION
INTERSUBTYPE RECOMBINATION
PRIMARY INFECTION
TARGET-CELLS
HOT-SPOTS
T-CELLS
SELECTION
GENOME
IDENTIFICATION
Summary BACKGROUND: HIV recombination has been estimated in vitro using a variety of approaches, and shows a high rate of template switching per reverse transcription event. In-vivo studies of recombination generally measure the accumulation of recombinant strains over time, and thus do not directly estimate a comparable template switching rate. METHOD: To examine whether the estimated in-vitro template switching rate is representative of the rate that occurs during HIV infection in vivo, we adopted a novel approach, analysing single genome sequences from early founder viruses to study the in-vivo template switching rate in the env region of HIV. RESULTS: We estimated the in-vivo per cycle template switching rate to be between 0.5 and 1.5/1000 nt, or approximately 5-14 recombination events over the length of the HIV genome. CONCLUSION: The in-vivo estimated template switching rate is close to the in-vitro estimated rate found in primary T lymphocytes but not macrophages, which is consistent with the majority of HIV infection occurring in T lymphocytes.
Language eng
DOI 10.1097/QAD.0000000000000936
Field of Research 110804 Medical Virology
Socio Economic Objective 920109 Infectious Diseases
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Grant ID NHMRC 1025270
Copyright notice ©2016, Wolters Kluwer Health
Persistent URL http://hdl.handle.net/10536/DRO/DU:30080651

Document type: Journal Article
Collections: Faculty of Health
School of Medicine
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