Di Giallonardo Francesca, Pinto Angie N, Keen Phillip, Shaik Ansari, Carrera Alex, Salem Hanan, Selvey Christine, Nigro Steven J, Fraser Neil, Price Karen, Holden Joanne, Lee Frederick J, Dwyer Dominic E, Bavinton Benjamin R, Geoghegan Jemma L, Grulich Andrew E, Kelleher Anthony D
The Kirby Institute, The University of New South Wales, Sydney, NSW, Australia.
Royal Prince Alfred Hospital, Sydney, NSW, Australia.
J Int AIDS Soc. 2021 Jan;24(1):e25655. doi: 10.1002/jia2.25655.
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.
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.
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.
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.
人类免疫缺陷病毒1型（HIV-1）大流行的特点是存在众多不同的子流行（集群），这些子流行持续推动着本地传播。本研究的目的是识别活跃增长的集群，了解哪些因素对传播动态影响最大，这些因素在不同亚型之间如何变化，以及这些信息如何有助于有效的公共卫生应对措施。
我们使用了与人口统计学因素相关的HIV-1基因组序列数据，这些数据占新南威尔士州（NSW）所有新HIV-1报告病例的约70%。我们评估了B亚型和循环重组形式01_AE（CRF01_AE）之间传播集群动态的差异。使用2004年至2018年期间采样的2919个B亚型和473个CRF01_AE序列结合全球序列数据估计单独的系统发育树，并将新南威尔士州特有的进化枝分类为集群、配对或单例。使用卡方统计评估亚型之间人口统计学的显著差异。
我们识别出104个B亚型和11个CRF01_AE增长集群，B亚型和CRF01_AE分别最多包含29个和11个序列。我们观察到新南威尔士州特有的CRF01_AE进化枝数量随时间增加了两倍多。B亚型集群与报告男男性行为者（MSM）为传播风险因素、出生在澳大利亚以及在感染早期被诊断出的个体相关（p<0.01）。CRF01_AE感染集群与在感染早期被诊断出的个体中的感染相关（p<0.05），CRF01_AE单例更可能来自报告异性传播的个体中的感染（p<0.05）。我们发现六个B亚型集群的增长率高于平均水平（>1.5个序列/6个月），且大多数感染发生在男男性行为者中。我们还发现四个活跃增长的CRF01_AE集群，仅包含男男性行为者中的感染。最后，我们发现47个B亚型和七个CRF01_AE集群，其感染之间存在较大的时间间隔（>1年），这可能表明存在通过未诊断个体的中间传播。
男男性行为者中大量活跃且增长的集群是新南威尔士州B亚型和CRF01_AE持续流行的驱动力。
