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New Genomes from the Congo Basin Expand History of CRF01_AE Origin and Dissemination.

  • Junqueira, Dennis Maletich1, 2, 3
  • Wilkinson, Eduan2, 3
  • Vallari, Ana4
  • Deng, Xianding5, 6
  • Achari, Asmeeta5, 6
  • Yu, Guixia5, 6
  • McArthur, Carole7
  • Kaptue, Lazare8
  • Mbanya, Dora9, 10
  • Chiu, Charles5, 6, 11
  • Cloherty, Gavin A4
  • de Oliveira, Tulio2, 3, 12
  • Rodgers, Mary A4
  • 1 Centro Universitário Ritter dos Reis-UniRitter, Porto Alegre, Brazil. , (Brazil)
  • 2 KwaZulu-Natal Research Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, Republic of South Africa. , (South Africa)
  • 3 School of Laboratory Medicine and Medical Science, College of Health Sciences, University of KwaZulu-Natal, Durban, Republic of South Africa. , (South Africa)
  • 4 Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, USA.
  • 5 Department of Laboratory Medicine, University of California, San Francisco, California, USA.
  • 6 UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • 7 School of Dentistry and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA.
  • 8 Université des Montagnes, Bangangté, Cameroon. , (Cameroon)
  • 9 Université de Yaoundé I, Yaoundé, Cameroon. , (Cameroon)
  • 10 University of Bamenda, Bamenda, Cameroon. , (Cameroon)
  • 11 Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California, USA.
  • 12 Research Department of Infection, University College London, London, United Kingdom. , (United Kingdom)
Published Article
AIDS Research and Human Retroviruses
Mary Ann Liebert
Publication Date
Jul 01, 2020
DOI: 10.1089/AID.2020.0031
PMID: 32281388


Although the first HIV circulating recombinant form (CRF01_AE) is the predominant strain in many Asian countries, it is uncommonly found in the Congo Basin from where it first originated. To fill the gap in the evolutionary history of this important strain, we sequenced near complete genomes from HIV samples with subgenomic CRF01_AE regions collected in Cameroon and the Democratic Republic of the Congo from 2001 to 2006. HIV genomes were generated from N = 13 plasma specimens by next-generation sequencing of metagenomic libraries prepared with spiked primers targeting HIV, followed by Sanger gap-filling. Genome sequences were aligned to reference strains, including Asian and African CRF01_AE sequences, and evaluated by phylogenetic and recombinant analysis to identify four CRF01_AE strains from Cameroon. We also identified two CRF02, one CRF27, and six unique recombinant form genomes (01|A1|G, 01|02|F|U, F|G|01, A1|D|01, F|G|01, and A1|G|01). Phylogenetic analysis, including the four new African CRF01_AE genomes, placed these samples as a bridge between basal Central African Republic CRF01_AE strains and all Asian, European, and American CRF01_AE strains. Molecular dating confirmed previous estimates indicating that the most recent common CRF01_AE ancestor emerged in the early 1970s (1968-1970) and spread beyond Africa around 1980 to Asia. The new sequences and analysis presented in this study expand the molecular history of the CRF01_AE clade, and are illustrated in an interactive Next Strain phylogenetic tree, map, and timeline at (

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