Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia
Francesca Di Giallonardo,
Angie N. Pinto,
Phillip Keen,
Ansari Shaik,
Alex Carrera,
Hanan Salem,
Barbara Telfer,
Craig Cooper,
Karen Price,
Christine Selvey,
Joanne Holden,
Nadine Bachmann,
Frederick J. Lee,
Dominic E. Dwyer,
Sebastián Duchêne,
Edward C. Holmes,
Andrew E. Grulich,
Anthony D. Kelleher
Affiliations
Francesca Di Giallonardo
The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia
Angie N. Pinto
The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia
Phillip Keen
The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia
Ansari Shaik
The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia
Alex Carrera
New South Wales State Reference Laboratory for HIV/AIDS, Darlinghurst, New South Wales 2010, Australia
Hanan Salem
New South Wales Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia
Barbara Telfer
Health Protection New South Wales, New South Wales Health, NSW, North Sydne, New South Wales 2060, Australia
Craig Cooper
Positive Life New South Wales, Surry Hills, New South Wales 2010, Australia
Karen Price
ACON Health Ltd., Surry Hills, New South Wales 2010, Australia
Christine Selvey
Health Protection New South Wales, New South Wales Health, NSW, North Sydne, New South Wales 2060, Australia
Joanne Holden
Centre for Population Health, New South Wales Ministry of Health, North Sydney, New South Wales 2059, Australia
Nadine Bachmann
Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland
Frederick J. Lee
New South Wales Health Pathology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia
Dominic E. Dwyer
New South Wales Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales 2145, Australia
Sebastián Duchêne
Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
Edward C. Holmes
Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
Andrew E. Grulich
The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia
Anthony D. Kelleher
The Kirby Institute, The University of New South Wales, Sydney, New South Wales 2052, Australia
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.
