A case of infection with a candidate new subtype, tentatively termed M, of human immunodeficiency virus type 1 of group M.
6 affiliations
- 1IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, 13005, France.
- 2Assistance Publique-Hôpitaux de Marseille (AP-HM), Laboratoire des Agents Infectieux, 19-21 boulevard Jean Moulin, Marseille, 13005, France.
- 3Aix-Marseille Univ., Microbes Evolution PHylogeny and Infections (MEPHI), UR D-258, 27 boulevard Jean Moulin, Marseille, 13005, France.
- 4Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital La Timone, Laboratoire de Pharmacocinétique et Toxicologie, Marseille, France.
- 5Assistance Publique-Hôpitaux de Marseille (AP-HM), Service de Maladies Infectieuses, 19-21 boulevard Jean Moulin, Marseille, 13005, France.
- 6Aix-Marseille Univ., Risques Infectieux Tropicaux Microorganismes ÉmergentS (RITMES), D257_UMR MD4, 27 boulevard Jean Moulin, Marseille, 13005, France.
Abstract
Background
HIV-1 emergence is estimated to have occurred c.a. 1920s in the Democratic Republic of the Congo (DRC). Only its group M is pandemic. It currently comprises 10 established subtypes. Here, we describe a near-complete HIV-1 genome that meets the definition of a candidate new subtype.Methods
In-house-designed or commercial PCR primers were used for amplification of HIV-1 DNA from blood. Sequencing used Sanger and next-generation (Oxford Nanopore, Illumina) technologies. Bioinformatic analyses used Samtools, Minimap2, Viroscore, Bootscan, IQ-TREE, iTOL, MEGA12, and Nextclade. Structural analyses used Mutate, HyperChem, and Molegro Molecular Viewer.Results
The patient originates from the DRC. CD4⁺ T cell counts fluctuated between 351 and 2394/mm3, and plasma viral load, initially 5.0 log₁₀copies/mL, reached undetectability on antiretroviral therapy. The obtained near-full length genome (PZ307881) showed a mean nucleotide divergence of 12.7% (range, 11.9-13.7%) with genomes of the 10 established subtypes, while mean divergence was 12.6% (10.0-13.7%) between these 10 subtypes. Phylogeny displayed a star-like tree topology. No recombination was identified. No natural antiretroviral drug resistance was detected. Reverse transcriptase (RT) structure exhibited slight changes compared to subtype B RT that could alter processivity and may favor increased genetic diversity.Conclusions
These data support a candidate new HIV-1 group M subtype we tentatively termed M pending official taxonomic classification. They indicate that HIV-1 diversity is still not comprehensively deciphered and are in line with the DRC as an epicenter of the HIV-1/M pandemic. They warrant further studies to establish this provisional candidate new subtype by detecting it in other epidemiologically unlinked individuals, and to assess its epidemiological, genotypic and phenotypic features.
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BibTeX
@article{colson2026case,
title = {{A case of infection with a candidate new subtype, tentatively termed M, of human immunodeficiency virus type 1 of group M.}},
author = {Philippe Colson and Céline Boschi and Marielle Bedotto and Anne Motte and Caroline Solas and Marine Lefebvre and Matthieu Million and Christelle Tomei and Jeremy Delerce and Jacques Fantini},
journal = {New microbes and new infections},
year = {2026},
month = oct,
doi = {10.1016/j.nmni.2026.101863},
url = {https://europepmc.org/article/MED/42927089},
note = {CC BY},
}
RIS
TY - JOUR
TI - A case of infection with a candidate new subtype, tentatively termed M, of human immunodeficiency virus type 1 of group M.
AU - Philippe Colson
AU - Céline Boschi
AU - Marielle Bedotto
AU - Anne Motte
AU - Caroline Solas
AU - Marine Lefebvre
AU - Matthieu Million
AU - Christelle Tomei
AU - Jeremy Delerce
AU - Jacques Fantini
PY - 2026
DA - 2026/10/09
JO - New microbes and new infections
DO - 10.1016/j.nmni.2026.101863
UR - https://europepmc.org/article/MED/42927089
AB - Background HIV-1 emergence is estimated to have occurred c.a. 1920s in the Democratic Republic of the Congo (DRC). Only its group M is pandemic. It currently comprises 10 established subtypes. Here, we describe a near-complete HIV-1 genome that meets the definition of a candidate new subtype.Methods In-house-designed or commercial PCR primers were used for amplification of HIV-1 DNA from blood. Sequencing used Sanger and next-generation (Oxford Nanopore, Illumina) technologies. Bioinformatic analyses used Samtools, Minimap2, Viroscore, Bootscan, IQ-TREE, iTOL, MEGA12, and Nextclade. Structural analyses used Mutate, HyperChem, and Molegro Molecular Viewer.Results The patient originates from the DRC. CD4⁺ T cell counts fluctuated between 351 and 2394/mm3, and plasma viral load, initially 5.0 log₁₀copies/mL, reached undetectability on antiretroviral therapy. The obtained near-full length genome (PZ307881) showed a mean nucleotide divergence of 12.7% (range, 11.9-13.7%) with genomes of the 10 established subtypes, while mean divergence was 12.6% (10.0-13.7%) between these 10 subtypes. Phylogeny displayed a star-like tree topology. No recombination was identified. No natural antiretroviral drug resistance was detected. Reverse transcriptase (RT) structure exhibited slight changes compared to subtype B RT that could alter processivity and may favor increased genetic diversity.Conclusions These data support a candidate new HIV-1 group M subtype we tentatively termed M pending official taxonomic classification. They indicate that HIV-1 diversity is still not comprehensively deciphered and are in line with the DRC as an epicenter of the HIV-1/M pandemic. They warrant further studies to establish this provisional candidate new subtype by detecting it in other epidemiologically unlinked individuals, and to assess its epidemiological, genotypic and phenotypic features.
SN - 2052-2975
ER -