A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism

Heather E. Grant; Sunando Roy; Rachel Williams; Helena Tutill; Bridget Ferns; Patricia A. Cane; J. Wilson Carswell; Deogratius Ssemwanga; Pontiano Kaleebu; Judith Breuer; Andrew J. Leigh Brown

doi:10.1186/s12977-022-00612-5

A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism

Heather E. Grant, Sunando Roy, Rachel Williams, Helena Tutill, Bridget Ferns, Patricia A. Cane, J. Wilson Carswell, Deogratius Ssemwanga, Pontiano Kaleebu, Judith Breuer, Andrew J. Leigh Brown

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller ‘intermediate’ genome dataset from 1998 to 1999 and a ‘modern’ genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p

Original language	English
Article number	28
Number of pages	10
Journal	Retrovirology
Volume	19
Issue number	1
DOIs	https://doi.org/10.1186/s12977-022-00612-5
Publication status	Published - 13 Dec 2022

Keywords / Materials (for Non-textual outputs)

HIV
subtype D
East Africa
co receptor
target capture sequencing
historic samples

Access to Document

10.1186/s12977-022-00612-5Licence: Creative Commons: Attribution (CC-BY)

BrownEtalR2022ALargePopulationSampleOfAfricanHIVFinal published version, 1.28 MBLicence: Creative Commons: Attribution (CC-BY)

Phylogenetics Networks to Address Tranmission of HIV
Leigh-Brown, A.
Other
18/10/13 → 30/09/17
Project: Research

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Grant, H. E., Roy, S., Williams, R., Tutill, H., Ferns, B., Cane, P. A., Carswell, J. W., Ssemwanga, D., Kaleebu, P., Breuer, J., & Leigh Brown, A. J. (2022). A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism. Retrovirology, 19(1), [28]. https://doi.org/10.1186/s12977-022-00612-5

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abstract = "We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller {\textquoteleft}intermediate{\textquoteright} genome dataset from 1998 to 1999 and a {\textquoteleft}modern{\textquoteright} genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p ",

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author = "Grant, {Heather E.} and Sunando Roy and Rachel Williams and Helena Tutill and Bridget Ferns and Cane, {Patricia A.} and Carswell, {J. Wilson} and Deogratius Ssemwanga and Pontiano Kaleebu and Judith Breuer and {Leigh Brown}, {Andrew J.}",

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doi = "10.1186/s12977-022-00612-5",

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AU - Grant, Heather E.

AU - Roy, Sunando

AU - Williams, Rachel

AU - Tutill, Helena

AU - Ferns, Bridget

AU - Cane, Patricia A.

AU - Carswell, J. Wilson

AU - Ssemwanga, Deogratius

AU - Kaleebu, Pontiano

AU - Breuer, Judith

AU - Leigh Brown, Andrew J.

PY - 2022/12/13

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AB - We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller ‘intermediate’ genome dataset from 1998 to 1999 and a ‘modern’ genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p

KW - HIV

KW - subtype D

KW - East Africa

KW - co receptor

KW - target capture sequencing

KW - historic samples

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DO - 10.1186/s12977-022-00612-5

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A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism

Abstract / Description of output

Keywords / Materials (for Non-textual outputs)

Access to Document

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Projects

Phylogenetics Networks to Address Tranmission of HIV

Cite this