Imperial College London


Faculty of Natural SciencesDepartment of Mathematics

Visiting Professor



+44 (0)20 7594 2647c.colijn Website




626Huxley BuildingSouth Kensington Campus






BibTex format

author = {Ratmann, O and Wymant, C and Colijn, C and Danaviah, S and Essex, M and Frost, S and Gall, A and von, Haeseler A and Kaleebu, P and Kendall, M and Kozlov, A and Manasa, J and Quang, Minh B and Moyo, S and Novitsky, V and Nsubuga, R and Pillay, S and Quinn, TC and Serwadda, D and Ssemwanga, D and Stamatakis, A and Trininopoulos, J and Wawer, M and Leigh, Brown A and de, Oliveira T and Kellam, P and Pillay, D and Fraser, C},
doi = {10.1089/AID.2017.0061},
journal = {Aids Research and Human Retroviruses},
pages = {1083--1098},
title = {HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences},
url = {},
volume = {33},
year = {2017}

RIS format (EndNote, RefMan)

AB - To characterize HIV-1 transmission dynamics in regions where the burden of HIV-1 is greatest, the “Phylogenetics and Networks for Generalised HIV Epidemics in Africa” consortium (PANGEA-HIV) is sequencing full-genome viral isolates from across sub-Saharan Africa. We report the first 3,985 PANGEA-HIV consensus sequences from four cohort sites (Rakai Community Cohort Study, n = 2,833; MRC/UVRI Uganda, n = 701; Mochudi Prevention Project, n = 359; Africa Health Research Institute Resistance Cohort, n = 92). Next-generation sequencing success rates varied: more than 80% of the viral genome from the gag to the nef genes could be determined for all sequences from South Africa, 75% of sequences from Mochudi, 60% of sequences from MRC/UVRI Uganda, and 22% of sequences from Rakai. Partial sequencing failure was primarily associated with low viral load, increased for amplicons closer to the 3′ end of the genome, was not associated with subtype diversity except HIV-1 subtype D, and remained significantly associated with sampling location after controlling for other factors. We assessed the impact of the missing data patterns in PANGEA-HIV sequences on phylogeny reconstruction in simulations. We found a threshold in terms of taxon sampling below which the patchy distribution of missing characters in next-generation sequences (NGS) has an excess negative impact on the accuracy of HIV-1 phylogeny reconstruction, which is attributable to tree reconstruction artifacts that accumulate when branches in viral trees are long. The large number of PANGEA-HIV sequences provides unprecedented opportunities for evaluating HIV-1 transmission dynamics across sub-Saharan Africa and identifying prevention opportunities. Molecular epidemiological analyses of these data must proceed cautiously because sequence sampling remains below the identified threshold and a considerable negative impact of missing characters on phyloge
AU - Ratmann,O
AU - Wymant,C
AU - Colijn,C
AU - Danaviah,S
AU - Essex,M
AU - Frost,S
AU - Gall,A
AU - von,Haeseler A
AU - Kaleebu,P
AU - Kendall,M
AU - Kozlov,A
AU - Manasa,J
AU - Quang,Minh B
AU - Moyo,S
AU - Novitsky,V
AU - Nsubuga,R
AU - Pillay,S
AU - Quinn,TC
AU - Serwadda,D
AU - Ssemwanga,D
AU - Stamatakis,A
AU - Trininopoulos,J
AU - Wawer,M
AU - Leigh,Brown A
AU - de,Oliveira T
AU - Kellam,P
AU - Pillay,D
AU - Fraser,C
DO - 10.1089/AID.2017.0061
EP - 1098
PY - 2017///
SN - 1931-8405
SP - 1083
TI - HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences
T2 - Aids Research and Human Retroviruses
UR -
UR -
VL - 33
ER -