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High frequency of new recombinant forms in HIV-1 transmission networks demonstrated by full genome sequencing

Laura Hebberecht, Virginie Mortier (UGent) , Kenny Dauwe (UGent) , Marlies Schauvliege (UGent) , Delfien Staelens (UGent) , Els Demecheleer (UGent) , Karolien Stoffels, Fien Vanroye, Marie-Luce Delforge, Ellen Vancutsem, et al.
(2020) INFECTION GENETICS AND EVOLUTION. 84.
Author
Organization
Abstract
The HIV-1 epidemic in Belgium is primarily driven by MSM. In this patient population subtype B predominates but an increasing presence of non-B subtypes has been reported. We aimed to define to what extent the increasing subtype heterogeneity in a high at risk population induces the formation and spread of new recombinant forms. The study focused on transmission networks that reflect the local transmission to an important extent. One hundred and five HIV-1 transmission clusters were identified after phylogenetic analysis of 2849 HIV-1 pol sequences generated for the purpose of baseline drug resistance testing between 2013 and 2017. Of these 105 clusters, 62 extended in size during the last two years and were therefore considered as representing ongoing transmission. These 62 clusters included 774 patients in total. From each cluster between 1 and 3 representative patients were selected for near full-length viral genome sequencing. In total, the full genome sequence of 101 patients was generated. Indications for the presence of a new recombinant form were found for 10 clusters. These 10 clusters represented 105 patients or 13.6% of the patients covered by the study. The findings clearly show that new recombinant strains highly contribute to local transmission, even in an epidemic that is largely MSM and subtype B driven. This is an evolution that needs to be monitored as reshuffiing of genome fragments through recombination may influence the transmissibility of the virus and the pathology of the infection. In addition, important changes in the sequence of the viral genome may challenge the performance of tests used for diagnosis, patient monitoring and drug resistance analysis.
Keywords
Microbiology (medical), Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Microbiology, Infectious Diseases, HIV-1, New recombinant forms, Transmission clusters, Full genome sequencing, Subtyping, PREVALENCE, SURVEILLANCE, DIVERSITY

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MLA
Hebberecht, Laura, et al. “High Frequency of New Recombinant Forms in HIV-1 Transmission Networks Demonstrated by Full Genome Sequencing.” INFECTION GENETICS AND EVOLUTION, vol. 84, 2020, doi:10.1016/j.meegid.2020.104365.
APA
Hebberecht, L., Mortier, V., Dauwe, K., Schauvliege, M., Staelens, D., Demecheleer, E., … Verhofstede, C. (2020). High frequency of new recombinant forms in HIV-1 transmission networks demonstrated by full genome sequencing. INFECTION GENETICS AND EVOLUTION, 84. https://doi.org/10.1016/j.meegid.2020.104365
Chicago author-date
Hebberecht, Laura, Virginie Mortier, Kenny Dauwe, Marlies Schauvliege, Delfien Staelens, Els Demecheleer, Karolien Stoffels, et al. 2020. “High Frequency of New Recombinant Forms in HIV-1 Transmission Networks Demonstrated by Full Genome Sequencing.” INFECTION GENETICS AND EVOLUTION 84. https://doi.org/10.1016/j.meegid.2020.104365.
Chicago author-date (all authors)
Hebberecht, Laura, Virginie Mortier, Kenny Dauwe, Marlies Schauvliege, Delfien Staelens, Els Demecheleer, Karolien Stoffels, Fien Vanroye, Marie-Luce Delforge, Ellen Vancutsem, Géraldine Dessilly, Dolorès Vaira, Kristel Van Laethem, and Chris Verhofstede. 2020. “High Frequency of New Recombinant Forms in HIV-1 Transmission Networks Demonstrated by Full Genome Sequencing.” INFECTION GENETICS AND EVOLUTION 84. doi:10.1016/j.meegid.2020.104365.
Vancouver
1.
Hebberecht L, Mortier V, Dauwe K, Schauvliege M, Staelens D, Demecheleer E, et al. High frequency of new recombinant forms in HIV-1 transmission networks demonstrated by full genome sequencing. INFECTION GENETICS AND EVOLUTION. 2020;84.
IEEE
[1]
L. Hebberecht et al., “High frequency of new recombinant forms in HIV-1 transmission networks demonstrated by full genome sequencing,” INFECTION GENETICS AND EVOLUTION, vol. 84, 2020.
@article{8693176,
  abstract     = {{The HIV-1 epidemic in Belgium is primarily driven by MSM. In this patient population subtype B predominates but an increasing presence of non-B subtypes has been reported. We aimed to define to what extent the increasing subtype heterogeneity in a high at risk population induces the formation and spread of new recombinant forms. The study focused on transmission networks that reflect the local transmission to an important extent. One hundred and five HIV-1 transmission clusters were identified after phylogenetic analysis of 2849 HIV-1 pol sequences generated for the purpose of baseline drug resistance testing between 2013 and 2017. Of these 105 clusters, 62 extended in size during the last two years and were therefore considered as representing ongoing transmission. These 62 clusters included 774 patients in total. From each cluster between 1 and 3 representative patients were selected for near full-length viral genome sequencing. In total, the full genome sequence of 101 patients was generated. Indications for the presence of a new recombinant form were found for 10 clusters. These 10 clusters represented 105 patients or 13.6% of the patients covered by the study. The findings clearly show that new recombinant strains highly contribute to local transmission, even in an epidemic that is largely MSM and subtype B driven. This is an evolution that needs to be monitored as reshuffiing of genome fragments through recombination may influence the transmissibility of the virus and the pathology of the infection. In addition, important changes in the sequence of the viral genome may challenge the performance of tests used for diagnosis, patient monitoring and drug resistance analysis.}},
  articleno    = {{104365}},
  author       = {{Hebberecht, Laura and Mortier, Virginie and Dauwe, Kenny and Schauvliege, Marlies and Staelens, Delfien and Demecheleer, Els and Stoffels, Karolien and Vanroye, Fien and Delforge, Marie-Luce and Vancutsem, Ellen and Dessilly, Géraldine and Vaira, Dolorès and Van Laethem, Kristel and Verhofstede, Chris}},
  issn         = {{1567-1348}},
  journal      = {{INFECTION GENETICS AND EVOLUTION}},
  keywords     = {{Microbiology (medical),Genetics,Ecology,Evolution,Behavior and Systematics,Molecular Biology,Microbiology,Infectious Diseases,HIV-1,New recombinant forms,Transmission clusters,Full genome sequencing,Subtyping,PREVALENCE,SURVEILLANCE,DIVERSITY}},
  language     = {{eng}},
  pages        = {{8}},
  title        = {{High frequency of new recombinant forms in HIV-1 transmission networks demonstrated by full genome sequencing}},
  url          = {{http://doi.org/10.1016/j.meegid.2020.104365}},
  volume       = {{84}},
  year         = {{2020}},
}
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