Abstract
IntroductionThe human immunodeficiency virus 1 (HIV‐1) pandemic is characterized by numerous distinct sub‐epidemics (clusters) that continually fuel local transmission. The aims of this study were to identify active growing clusters, to understand which factors most influence the transmission dynamics, how these vary between different subtypes and how this information might contribute to effective public health responses.MethodsWe used HIV‐1 genomic sequence data linked to demographic factors that accounted for approximately 70% of all new HIV‐1 notifications in New South Wales (NSW). We assessed differences in transmission cluster dynamics between subtype B and circulating recombinant form 01_AE (CRF01_AE). Separate phylogenetic trees were estimated using 2919 subtype B and 473 CRF01_AE sequences sampled between 2004 and 2018 in combination with global sequence data and NSW‐specific clades were classified as clusters, pairs or singletons. Significant differences in demographics between subtypes were assessed with Chi‐Square statistics.ResultsWe identified 104 subtype B and 11 CRF01_AE growing clusters containing a maximum of 29 and 11 sequences for subtype B and CRF01_AE respectively. We observed a > 2‐fold increase in the number of NSW‐specific CRF01_AE clades over time. Subtype B clusters were associated with individuals reporting men who have sex with men (MSM) as their transmission risk factor, being born in Australia, and being diagnosed during the early stage of infection (p < 0.01). CRF01_AE infections clusters were associated with infections among individuals diagnosed during the early stage of infection (p < 0.05) and CRF01_AE singletons were more likely to be from infections among individuals reporting heterosexual transmission (p < 0.05). We found six subtype B clusters with an above‐average growth rate (>1.5 sequences / 6‐months) and which consisted of a majority of infections among MSM. We also found four active growing CRF01_AE clusters containing only infections among MSM. Finally, we found 47 subtype B and seven CRF01_AE clusters that contained a large gap in time (>1 year) between infections and may be indicative of intermediate transmissions via undiagnosed individuals.ConclusionsThe large number of active and growing clusters among MSM are the driving force of the ongoing epidemic in NSW for subtype B and CRF01_AE.
Highlights
The human immunodeficiency virus 1 (HIV-1) pandemic is characterized by numerous distinct sub-epidemics that continually fuel local transmission
It is not surprising that we found that the majority of subtype B infections that were reported to have been acquired within Australia were in Australian-born individuals, and were characterized by numerous local transmission clusters, all of which is expected for an established endemic disease
We report on subtype-specific transmission dynamics with subtype B being dominated by larger clusters and CRF01_AE by sequence pairs
Summary
Australia is at the forefront of successful control of human immunodeficiency virus type 1 (HIV-1) transmission due to rapid and comprehensive public health responses from the beginning of the epidemic in the 1980s. The fine detail of transmission dynamics of HIV-1 in Australia is not well understood, as current surveillance reports rely on basic demographic data alone and do not include molecular epidemiological data [1]. It is not known if the subtype B epidemic is characterized by many small transmission clusters, as often observed in other countries [11], or fewer but larger sub-epidemics that are more common in regions with less population migration [12]. We performed phylogenetic analyses to identify sequence clusters that represent sub-epidemics in the two most common HIV-1 subtypes B and CRF01_AE [14] and followed the transmission dynamics in these clusters across a five-year time period
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