ABOUT PANGEA

PANGEA 1 review

PANGEA 2 review

Phylogenetics BASICS

Short introduction to phylogenetics

How to read a tree

Single-sex pairs in phylogenetic source attribution analyses

Ethics of phylogenetics

PANGEA phylogenetics course

Sequencing Protocols

PANGEA 1: Gall et al

PANGEA 2: Bonsall et al

BIOINFORMATICS PIPELINE

The raw sequence data is processed by a bespoke PANGEA Snakemake pipeline. The workflow includes raw data preprocessing, genome assembly with shiver, multiple alignment with iqtree, extraction of drug resistance data from the Stanford University HIV Drug Resistance Database HIVDB using sierralocal, and several quality assurance steps. Click here to see the workflow in a directed acyclic graph (DAG).

Webinars

Explainer Sessions - COnsortium Meeting 2020

Publications

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.

Ratmann O, Kagaayi J, Hall M, Golubchick T, Kigozi G, Xi X, Wymant C, Nakigozi G, Abeler-Dörner L, Bonsall D, Gall A, Hoppe A, Kellam P, Bazaale J, Kalibbala S, Laeyendecker O, Lessler J, Nalugoda F, Chang LW, de Oliveira T, Pillay D, Quinn TC, Reynolds SJ, Spencer SEF, Ssekubugu R, Serwadda D, Wawer MJ, Gray RH, Fraser C, Grabowski MK; Rakai Health Sciences Program and the Pangea HIV Consortium (2020). Lancet HIV pii: S2352-3018(19)30378-9

PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa.

Abeler-Dörner L, Grabowski KM, Rambaut A, Pillay D, Fraser C (2019). Curr Opin HIV AIDS 14, 173–180

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.

Ratmann O, Groabowski KM, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Leigh Brown A, de Oliveria T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C on behalf of the PANGEA consortium and the Rakai Health Sciences Program (2019). Nat Commun 10, 1411

Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations.

Bbosa N, Ssemwanga D, Nsubuga RN, Salazar-Gonzalez JF, Salazar MG, Nanyonjo M, Kuteesa M, Seeley J, Kiwanuka N, Bagaya BS, Yebra G, Leigh-Brown A, Kaleebu P (2019). Sci Rep 9, 1051

A comprehensive genomics solution for HIV surveillance and clinical monitoring in a global health setting.

Bonsall D, Golubchik T, de Cesare M,, Limbada M, Kosloff B, MacIntyre-Cockett G, Hall M, Wymant C, Ansari A, Abeler-Dörner L, Schaap, A, Borwn A, Bares E, Piwowar-Manning E, Wilson E, Emel L, Hayes R, Fidler S, Ayles H, Bowden R, Fraser C (2018). BioRxiv, 397083

Ethical considerations in global HIV phylogenetic research.

Coltart CEM, Hoppe A, Parker M, Dawson L, Amon JJ, Simwinga M, Geller G, Henderson G, Laeyendecker O, Tucker JD, Eba P, Novitsky V, Vandamme AM, Seeley J, Dallabetta G, Harling G, Grabowski MK, Godfrey-Faussett P, Fraser C, Cohen MS, Pillay D; Ethics in HIV Phylogenetics Working Group (2018). Lancet HIV 5: e656-e666

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Croucher NJ, Hall M, Hillebregt M, Ong SH, Ratmann O, Albert J, Bannert N, Fellay J, Fransen K, Gourlay A, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Cornelissen M, Kellam P, Reiss P, Fraser C; BEEHIVE Collaboration (2018).
Virus Evol 4, vey007

PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.

Wymant C, Hall M, Ratmann O, Bonsall D, Golubchik T, de Cesare M, Gall A, Cornelissen M, Fraser C; STOP-HCV Consortium, The Maela Pneumococcal Collaboration, and The BEEHIVE Collaboration (2017). Mol Biol Evol 35, 719-733

HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.

Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SDW, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Leigh Brown A, de Oliveira T, Kellam P, Pillay D, Fraser C (2017). AIDS Res Hum Retroviruses 33, 1083-1098

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C; PANGEA-HIV Consortium (2017). Mol Biol Evol 34, 185-3203

Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic.

Yebra G, Hodcroft EB, Ragonnet-Cronin ML, Pillay D, Brown AJ; PANGEA_HIV Consortium; ICONIC Project (2016). Sci Rep 23, 39489

PANGEA-HIV: phylogenetics for generalised epidemics in Africa.

Pillay D, Herbeck J, Cohen MS, de Oliveira T, Fraser C, Ratmann O, Brown AL, Kellam P; PANGEA-HIV Consortium (2015). Lancet Infect Dis 15, 259-6

Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes.

Gall A, Ferns B, Morris C, Watson S, Cotten M, Robinson M, Berry N, Pillay D, Kellam P. (2012)
J Clin Microbiol 50, 3838-44