Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia

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.

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

“…In contrast, CRF01_AE, similar to other non-B subtypes, is historically associated with heterosexual contact and acquisition outside Australia [28]. In our study, CRF01_AE was characterized by numerous sequence pairs and a majority of infections being singletons, which is more indicative of multiple introductions with only limited ongoing transmission [14]. This finding was supported by the associated demographic data, with a majority of these infections reported to be acquired outside Australia, and among individuals born in Asia.…”

“…The NSW HIV-1 database contains all protease, reverse transcriptase and integrase sequences sampled in NSW between 2004 and 2018. The HIV-1 subtype for these sequences was determined using the Stanford HIV subtyping tool [15,16] and confirmed by phylogeny, as described previously [14]. Only the first available sequence for each individual covering the protease and reverse transcriptase and that were classified as subtype B and CRF01_AE were included in the analysis.…”

“…An internal R script was used to extract clades within the phylogeny that only contained sequences from NSW, that is were monophyletic [14,17]. NSW-specific sequences that fell into neither category were defined as singletons (Figure S1).…”

“…The aim of this study was to understand changes in cluster dynamics over time in NSW. 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.…”

Phylogenetic clustering networks among heterosexual migrants with new HIV diagnoses post-migration in Australia

“…Molecular epidemiology, including phylogenetic analysis, is increasingly being used as to monitor and characterise HIV transmission and inform public health and prevention responses [11][12][13][14]. Molecular epidemiology has also been used to demonstrate increases in non-B subtypes in Australia and several European countries [15][16][17][18][19][20][21][22][23], and to estimate the number of infections likely to have been acquired post-migration in some cases [22]. However, these studies have not examined the characteristics of phylogenetic clusters, beyond using them to determine acquisition post-migration.…”