RESUMO
Shenzhen, a city with >12 million migrant population, may play a key role in the spread of human immunodeficiency virus (HIV)-1 in China. The transmission dynamics of CRF01_AE, a predominant subtype in Shenzhen, is a good model to characterize the impact of human mobility on HIV-1 epidemic locally and nationally. We used phylodynamic and phylogeographic methods to estimate the viral transmission dynamics and migration trajectory of variable lineages based on 1,423 CRF01_AE sequences in Shenzhen sampled between 2006 and 2015. Eleven lineages of CRF01_AE were detected in Shenzhen. Of those, four main lineages originated during the 1990s. Their basic viral reproduction number (R 0) ranged 1.96-3.92. The effective viral reproduction number (R e ) of two lineages prevalent among heterosexuals/people who inject drugs had reduced <1 at the end of sampling, and the main sources were the intra-provincial immigrants (72 per cent) for one and local residents of Shenzhen (91 per cent) for another. Within two lineages among men who have sex with men (MSM), R e had been above or close to 1 at the end of sampling, and the immigrants from Jiangxi/Shaanxi and Hubei as sources accounted for 93 per cent and 68 per cent of all viral migration events, respectively. Moreover, no obvious recipients were found throughout the viral migration history for any lineage. Our findings demonstrate that HIV epidemic is declining in Shenzhen, which coincided with the initiation of the interventions during the 2000s. However, the obvious differences of the epidemic patterns between lineages emphasize the importance of further targeting interventions and continued molecular tracing, focusing on high-risk transmission sources among MSM.
RESUMO
Australia's response to the human immunodeficiency virus type 1 (HIV-1) pandemic led to effective control of HIV transmission and one of the world's lowest HIV incidence rates-0.14%. Although there has been a recent decline in new HIV diagnoses in New South Wales (NSW), the most populous state in Australia, there has been a concomitant increase with non-B subtype infections, particularly for the HIV-1 circulating recombinant form CRF01_AE. This aforementioned CRF01_AE sampled in NSW, were combined with those sampled globally to identify NSW-specific viral clades. The population growth of these clades was assessed in two-year period intervals from 2009 to 2017. Overall, 109 NSW-specific clades were identified, most comprising pairs of sequences; however, five large clades comprising ≥10 sequences were also found. Forty-four clades grew over time with one or two sequences added to each in different two-year periods. Importantly, while 10 of these clades have seemingly discontinued, the remaining 34 were still active in 2016/2017. Seven such clades each comprised ≥10 sequences, and are representative of individual sub-epidemics in NSW. Thus, although the majority of new CRF01_AE infections were associated with small clades that rarely establish ongoing chains of local transmission, individual sub-epidemics are present and should be closely monitored.