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

1
The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia
2
Department of Infectious Diseases & Microbiology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia
3
New South Wales State Reference Laboratory for HIV/AIDS, Darlinghurst, New South Wales 2010, Australia
4
New South Wales Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia
5
Health Protection New South Wales, New South Wales Health, NSW, North Sydne, New South Wales 2060, Australia
6
Positive Life New South Wales, Surry Hills, New South Wales 2010, Australia
7
ACON Health Ltd., Surry Hills, New South Wales 2010, Australia
8
Centre for Population Health, New South Wales Ministry of Health, North Sydney, New South Wales 2059, Australia
9
Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland
10
Department of Clinical Immunology & Allergy, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia
11
Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
12
New South Wales Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales 2145, Australia
13
Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
14
Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
*
Author to whom correspondence should be addressed.
Viruses 2019, 11(5), 482; https://doi.org/10.3390/v11050482
Received: 12 April 2019 / Revised: 21 May 2019 / Accepted: 24 May 2019 / Published: 27 May 2019
(This article belongs to the Section Animal Viruses)
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. View Full-Text
Keywords: HIV-1 CRF01_AE; transmission cluster; evolution; cluster growth; sub-epidemic HIV-1 CRF01_AE; transmission cluster; evolution; cluster growth; sub-epidemic
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Di Giallonardo, F.; Pinto, A.N.; Keen, P.; Shaik, A.; Carrera, A.; Salem, H.; Telfer, B.; Cooper, C.; Price, K.; Selvey, C.; Holden, J.; Bachmann, N.; Lee, F.J.; Dwyer, D.E.; Duchêne, S.; Holmes, E.C.; Grulich, A.E.; Kelleher, A.D. Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia. Viruses 2019, 11, 482.

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