Subtype‐specific differences in transmission cluster dynamics of HIV‐1 B and CRF01_AE in New South Wales, Australia

Abstract

Introduction The 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. Methods We 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. Results We 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. Conclusions The 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.

Phylodynamic analysis reveals changing transmission dynamics of HIV-1 CRF01_AE in Japan from heterosexuals to men who have sex with men

“…Our analysis revealed that the transmission network of CRF01_AE in Japan has become more complex, comprizing predominantly MSM clusters along with persisting heterosexual/IDU-related clusters. This finding was consistent with a previous study from Australia, which is in the same Western Pacific region (Di Giallonardo et al, 2021). However, at the time of our study, it was not applicable to the European region, where heterosexuals still dominate the transmission network of CRF01_AE (Alexiev et al, 2021;Esbjornsson et al, 2016).…”

Association of demographics, HCV co‐infection, HIV‐1 subtypes and genetic clustering with late HIV diagnosis: a retrospective analysis from the Japanese Drug Resistance HIV‐1 Surveillance Network

“…Descriptive epidemiology of the national AIDS surveillance (NAS) in Japan showed that compared to individuals newly diagnosed with HIV without AIDS‐defining illnesses, those newly diagnosed with HIV and AIDS‐defining illnesses were more likely to be older, heterosexual and from non‐urban areas [ 10 ]. Besides demographics, hepatitis B or C co‐infections [ 19 , 20 ], HIV‐1 subtypes [ 21 , 22 , 23 ] and clustering based on nucleotide sequences [ 24 , 25 ] may be associated with late diagnosis, but this information is not included in the NAS. To our knowledge, no large‐scale nationwide study has revealed the association of the aforementioned factors with late HIV diagnosis.…”

Exploring and Predicting the Drivers of Ongoing HIV-1 Transmission in Guangyuan, Sichuan

“…An early study also reported that MSM transmission was be the main risk factor for transmission clusters. 39 Besides, as the characteristics of convenient transportation and mobility of downtown, which can lead to the further rapid spread of CRF07_BC in this area, further confirming that attention should be paid to the MSM, especially those live in downtown. We can continue to use the internet to carry out continuous online health education, condom promotion, AIDS counseling, mobilization testing and other services for MSM in Guangyuan, and even consider promoting pre-exposure prophylactics and other measures, so as to reduce the HIV transmission among MSM.…”