Background:  The period following primary HIV-1 infection may account for a significant proportion of new transmission events. This study characterized the interrelationships of viral sequences from all genotyped, recent infections in Quebec (1999-2005).    

Methods:  Sequence data were complied from the 2 provincial testing laboratories (2001-2005) and the Quebec Primary HIV-1 Infection cohort study (1998-2005). Phylogenetic tree analysis determined sequence interrelationships of all recent infections, identifying clustered transmission events and non-B subtype infections (n = 692). Clinical information on age, sex, route of transmission, and time of infection was obtained from questionnaires or validated genotypic test requisitions.

Results:  Half of subtype B infections in recently infected persons in Quebec are present in transmission clusters having 2 to 14 persons/cluster. The median and mean transmission interval for the 75 identified transmission clusters were 8±4.5 months and 10.8±1.1 months, respectively. Clustering was related with high-risk sexual behavior, wherein 40% of male-sex-male clusters included persons having sex with >5 persons in the 3-month interval prior to their diagnosis. The 35-55 age-groups were the at-risk population for subtype B infections. Non-B subtypes represented 16% of new infections in Quebec, with subtype C (51%), A/CRF1 (18%), G/CRF2/CRF6 (18%), D (8%), F (1%), and K/J CRF (5%) distribution. Non-B infections rarely represented clustered transmission events. Reported so far have been 7 primary non-B transmissions, including 2 subtype C, 4 CRF2, and 1 CRF1 infection.

Conclusions:  Routine genotyping is important for screening HIV-1 transmission and the spread of non-B infections, as well as for drug-resistance testing. Acute/early infection accounted for at least half of all reported subtype B transmissions. Non-B subtype infections are being rapidly introduced into Quebec, and public health policies must address evolving trends in HIV-1 transmission.