Abstract
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.
Highlights
The human immunodeficiency virus type 1 (HIV-1) is still a major burden worldwide with approximately 36.9 million individuals infected with HIV globally (WHO)
HIV-1 circulates globally as different genetically defined subtypes, the subtype prevalence varies across different countries; subtype C is most prevalent in Africa, the circulating recombinant form 01_AE (CRF01_AE) is most prevalent in Southeast Asia, and subtype B is most prevalent in the USA, Europe, and Australia [8]
This is of current importance because the HIV-1 epidemic in Australia is experiencing a shift in subtype incidence with a major increase in non-B
Summary
The human immunodeficiency virus type 1 (HIV-1) is still a major burden worldwide with approximately 36.9 million individuals infected with HIV globally (WHO). HIV-1 circulates globally as different genetically defined subtypes, the subtype prevalence varies across different countries; subtype C is most prevalent in Africa (and globally), the circulating recombinant form 01_AE (CRF01_AE) is most prevalent in Southeast Asia, and subtype B is most prevalent in the USA, Europe, and Australia [8]. This is of current importance because the HIV-1 epidemic in Australia is experiencing a shift in subtype incidence with a major increase in non-B infections, as an estimated 20% of all new infections in Australia were of non-B origin in 2006, and that increased to 38% in 2016 [9]. To better understand the phylodynamics of CRF01_AE in NSW we (i) identified independent transmission clades, (ii) estimated clade growth over time, and (iii) assessed the impact of transmission clade growth on the NSW epidemic
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