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

HIV-1 epidemic in Belgium mainly driven by the MSM. In these patients subtype B predominates but the presence of an increase in population of non-B subtypes have been reported. We aimed to determine the extent to which the increase in the heterogeneity of subtypes in high risk populations induces the formation and deployment of a new recombinant form. This study focused on the transmission network which reflects the local transmission to the important ones.

One hundred and five HIV-1 transmission clusters were identified after 2849 phylogenetic analysis of HIV-1 pol sequences generated for the purpose of drug resistance test basis between 2013 and 2017. Of this group 105, 62 extended in size over the last two years and therefore considered as representing continuous transmission. These 62 clusters including 774 patients in total. From each cluster between 1 and 3 patient representatives have been selected to close the full-length viral genome sequencing. In total, 101 patients full genome sequence generated. Indications for the presence of recombinant forms newfound to 10 clusters.

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These 10 clusters represented 105 patients or 13.6% of the patients covered by the study. The findings clearly show that the new recombinant strains that contribute to local transmission, even in epidemic largely driven MSM and subtype B. It is an evolution that needs to be monitored as a genomic fragment reshuffled through recombination can affect the transmissibility of viruses and pathology of infection. In addition, important changes in the virus genome sequence can be challenging performance tests used for diagnosis, patient monitoring and analysis of drug resistance.

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