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Article ; Online: Recovery of yellow fever virus whole genome from an individual with severe vaccine-associated viscerotropic disease.

Walker, Harry N / Caly, Leon / Savic, Ivana / Aziz, Ammar / Tran, Thomas / Whitley, Megan / Chavada, Ruchir / Lim, Chuan Kok

The Lancet. Microbe

2024

Language	English
Publishing date	2024-01-11
Publishing country	England
Document type	Letter
ISSN	2666-5247
ISSN (online)	2666-5247
DOI	10.1016/S2666-5247(23)00395-6
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Article ; Online: A real-time PCR assay for Japanese encephalitis virus (JEV) genotype IV as a public health laboratory response to an emerging outbreak in Australia.

Martin, Genevieve E / Tran, Thomas / Papadakis, Georgina / Kinsella, Paul / Druce, Julian / Caly, Leon / Williamson, Deborah A / Lim, Chuan Kok

Pathology

2023 Volume 55, Issue 6, Page(s) 869–870

MeSH term(s)	Humans ; Encephalitis Virus, Japanese/genetics ; Real-Time Polymerase Chain Reaction ; Public Health ; Genotype ; Disease Outbreaks
Language	English
Publishing date	2023-04-11
Publishing country	England
Document type	Letter
ZDB-ID	7085-3
ISSN	1465-3931 ; 0031-3025
ISSN (online)	1465-3931
ISSN	0031-3025
DOI	10.1016/j.pathol.2023.02.006
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Zs.A 723: Show issues

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Article ; Online: A Case of Congenital Human Parechovirus Type 3 Meningoencephalitis.

Mei Jy Lim, Selina / Foley, David Anthony / Lakshmanan, Rahul / Caly, Leon / Gehlot, Sanjay / Davis, Jonathan

The Pediatric infectious disease journal

2022 Volume 41, Issue 2, Page(s) e67–e68

MeSH term(s)	Adult ; Cerebral Palsy ; Cesarean Section ; Female ; Humans ; Infant, Newborn ; Meningoencephalitis/congenital ; Meningoencephalitis/therapy ; Meningoencephalitis/virology ; Parechovirus/genetics ; Parechovirus/isolation & purification ; Picornaviridae Infections/congenital ; Picornaviridae Infections/therapy ; Picornaviridae Infections/virology ; Pregnancy ; Seizures ; Tachycardia
Language	English
Publishing date	2022-01-11
Publishing country	United States
Document type	Case Reports ; Letter
ZDB-ID	392481-6
ISSN	1532-0987 ; 0891-3668
ISSN (online)	1532-0987
ISSN	0891-3668
DOI	10.1097/INF.0000000000003369
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Zs.A 1852: Show issues

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Article ; Online: Lymphocytic Choriomeningitis Virus Infection, Australia.

Caly, Leon / Porter, Ashleigh F / Chua, Joanna / Collet, James P / Druce, Julian D / Catton, Michael G / Duchene, Sebastian

Emerging infectious diseases

2022 Volume 28, Issue 8, Page(s) 1713–1715

Abstract: During a mouse plague in early 2021, a farmer from New South Wales, Australia, sought treatment for aseptic meningitis and was subsequently diagnosed with locally acquired lymphocytic choriomeningitis virus infection. Whole-genome sequencing identified a ...

Abstract	During a mouse plague in early 2021, a farmer from New South Wales, Australia, sought treatment for aseptic meningitis and was subsequently diagnosed with locally acquired lymphocytic choriomeningitis virus infection. Whole-genome sequencing identified a divergent and geographically distinct lymphocytic choriomeningitis virus strain compared with other published sequences.
MeSH term(s)	Animals ; Australia/epidemiology ; Lymphocytic Choriomeningitis/diagnosis ; Lymphocytic Choriomeningitis/epidemiology ; Lymphocytic choriomeningitis virus/genetics ; Meningitis, Aseptic ; Mice ; New South Wales/epidemiology
Language	English
Publishing date	2022-07-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2808.220119
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Zs.A 4778: Show issues

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Article ; Online: The FDA-approved drug ivermectin inhibits the replication of SARS-CoV-2 in vitro.

Caly, Leon / Druce, Julian D / Catton, Mike G / Jans, David A / Wagstaff, Kylie M

Antiviral research

2020 Volume 178, Page(s) 104787

Abstract: Although several clinical trials are now underway to test possible therapies, the worldwide response to the COVID-19 outbreak has been largely limited to monitoring/containment. We report here that Ivermectin, an FDA-approved anti-parasitic previously ... ...

Abstract	Although several clinical trials are now underway to test possible therapies, the worldwide response to the COVID-19 outbreak has been largely limited to monitoring/containment. We report here that Ivermectin, an FDA-approved anti-parasitic previously shown to have broad-spectrum anti-viral activity in vitro, is an inhibitor of the causative virus (SARS-CoV-2), with a single addition to Vero-hSLAM cells 2 h post infection with SARS-CoV-2 able to effect ~5000-fold reduction in viral RNA at 48 h. Ivermectin therefore warrants further investigation for possible benefits in humans.
MeSH term(s)	Animals ; Antiviral Agents/pharmacology ; Australia ; Betacoronavirus/drug effects ; Betacoronavirus/physiology ; COVID-19 ; Chlorocebus aethiops ; Coronavirus Infections/drug therapy ; Coronavirus Infections/virology ; Drug Approval ; Humans ; Ivermectin/pharmacology ; Ivermectin/therapeutic use ; Pandemics ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/virology ; SARS-CoV-2 ; Vero Cells ; Virus Replication/drug effects
Chemical Substances	Antiviral Agents ; Ivermectin (70288-86-7)
Keywords	covid19
Language	English
Publishing date	2020-04-03
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	306628-9
ISSN	1872-9096 ; 0166-3542
ISSN (online)	1872-9096
ISSN	0166-3542
DOI	10.1016/j.antiviral.2020.104787
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Zs.A 1627: Show issues

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Article ; Online: Analytical Sensitivity of Lateral Flow Devices against SARS-CoV-2 Omicron Subvariants BA.4, BA.5, and BA.2.75.

Mackenzie, Charlene / Batty, Mitchell / Papadakis, Georgina / Stevens, Laura / Yoga, Yano / Taiaroa, George / Stefanatos, Helen / Savic, Ivana / Tran, Thomas / Deerain, Joshua / Prestedge, Jacqueline / Druce, Julian / Caly, Leon / Williamson, Deborah A

Journal of clinical microbiology

2022 Volume 60, Issue 11, Page(s) e0109722

MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Antibodies, Viral ; Cell Line
Chemical Substances	Antibodies, Viral
Language	English
Publishing date	2022-10-31
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/jcm.01097-22
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Zs.A 1188: Show issues

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Article ; Online: Maintaining genomic surveillance using whole-genome sequencing of SARS-CoV-2 from rapid antigen test devices.

Martin, Genevieve E / Taiaroa, George / Taouk, Mona L / Savic, Ivana / O'Keefe, Jacinta / Quach, Robert / Prestedge, Jacqueline / Krysiak, Marcelina / Caly, Leon / Williamson, Deborah A

The Lancet. Infectious diseases

2022 Volume 22, Issue 10, Page(s) 1417–1418

MeSH term(s)	COVID-19/diagnosis ; Genome, Viral ; Genomics ; Humans ; SARS-CoV-2/genetics ; Whole Genome Sequencing
Language	English
Publishing date	2022-08-04
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	2061641-7
ISSN	1474-4457 ; 1473-3099
ISSN (online)	1474-4457
ISSN	1473-3099
DOI	10.1016/S1473-3099(22)00512-6
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Zs.A 5743: Show issues

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Article ; Online: Intra- and interhost genomic diversity of monkeypox virus.

Taouk, Mona L / Steinig, Eike / Taiaroa, George / Savic, Ivana / Tran, Thomas / Higgins, Nasra / Tran, Stephanie / Lee, Alvin / Braddick, Maxwell / Moso, Michael A / Chow, Eric P F / Fairley, Christopher K / Towns, Janet / Chen, Marcus Y / Caly, Leon / Lim, Chuan K / Williamson, Deborah A

Journal of medical virology

2023 Volume 95, Issue 8, Page(s) e29029

Abstract: The impact and frequency of infectious disease outbreaks demonstrate the need for timely genomic surveillance to inform public health responses. In the largest known outbreak of mpox, genomic surveillance efforts have primarily focused on high-incidence ... ...

Abstract	The impact and frequency of infectious disease outbreaks demonstrate the need for timely genomic surveillance to inform public health responses. In the largest known outbreak of mpox, genomic surveillance efforts have primarily focused on high-incidence nations in Europe and the Americas, with a paucity of data from South-East Asia and the Western Pacific. Here we analyzed 102 monkeypox virus (MPXV) genomes sampled from 56 individuals in Melbourne, Australia. All genomes fell within the 2022 MPXV outbreak lineage (B.1), with likely onward local transmission detected. We observed within-host diversity and instances of co-infection, and highlight further examples of structural variation and apolipoprotein B editing complex-driven micro-evolution in the current MPXV outbreak. Updating our understanding of MPXV emergence and diversification will inform public health measures and enable monitoring of the virus' evolutionary trajectory throughout the mpox outbreak.
MeSH term(s)	Humans ; Monkeypox virus/genetics ; Mpox (monkeypox)/epidemiology ; Genomics ; Disease Outbreaks ; Australia/epidemiology
Language	English
Publishing date	2023-08-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.29029
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Zs.A 1320: Show issues

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Article ; Online: Non-SARS-CoV-2 respiratory viral detection and whole genome sequencing from COVID-19 rapid antigen test devices: a laboratory evaluation study.

The Lancet. Microbe

2024 Volume 5, Issue 4, Page(s) e317–e325

Abstract: Background: There has been high uptake of rapid antigen test device use for point-of-care COVID-19 diagnosis. Individuals who are symptomatic but test negative on COVID-19 rapid antigen test devices might have a different respiratory viral infection. We ...

Abstract	Background: There has been high uptake of rapid antigen test device use for point-of-care COVID-19 diagnosis. Individuals who are symptomatic but test negative on COVID-19 rapid antigen test devices might have a different respiratory viral infection. We aimed to detect and sequence non-SARS-CoV-2 respiratory viruses from rapid antigen test devices, which could assist in the characterisation and surveillance of circulating respiratory viruses in the community. Methods: We applied archival clinical nose and throat swabs collected between Jan 1, 2015, and Dec 31, 2022, that previously tested positive for a common respiratory virus (adenovirus, influenza, metapneumovirus, parainfluenza, rhinovirus, respiratory syncytial virus [RSV], or seasonal coronavirus; 132 swabs and 140 viral targets) on PCR to two commercially available COVID-19 rapid antigen test devices, the Panbio COVID-19 Ag Rapid Test Device and Roche SARS-CoV-2 Antigen Self-Test. In addition, we collected 31 COVID-19 rapid antigen test devices used to test patients who were symptomatic at The Royal Melbourne Hospital emergency department in Melbourne, Australia. We extracted total nucleic acid from the device paper test strips and assessed viral recovery using multiplex real-time PCR (rtPCR) and capture-based whole genome sequencing. Sequence and genome data were analysed through custom computational pipelines, including subtyping. Findings: Of the 140 respiratory viral targets from archival samples, 89 (64%) and 88 (63%) were positive on rtPCR for the relevant taxa following extraction from Panbio or Roche rapid antigen test devices, respectively. Recovery was variable across taxa: we detected influenza A in nine of 18 samples from Panbio and seven of 18 from Roche devices; parainfluenza in 11 of 20 samples from Panbio and 12 of 20 from Roche devices; human metapneumovirus in 11 of 16 from Panbio and 14 of 16 from Roche devices; seasonal coronavirus in eight of 19 from Panbio and two of 19 from Roche devices; rhinovirus in 24 of 28 from Panbio and 27 of 28 from Roche devices; influenza B in four of 15 in both devices; and RSV in 16 of 18 in both devices. Of the 31 COVID-19 devices collected from The Royal Melbourne Hospital emergency department, 11 tested positive for a respiratory virus on rtPCR, including one device positive for influenza A virus, one positive for RSV, four positive for rhinovirus, and five positive for SARS-CoV-2. Sequences of target respiratory viruses from archival samples were detected in 55 (98·2%) of 56 samples from Panbio and 48 (85·7%) of 56 from Roche rapid antigen test devices. 98 (87·5%) of 112 viral genomes were completely assembled from these data, enabling subtyping for RSV and influenza viruses. All 11 samples collected from the emergency department had viral sequences detected, with near-complete genomes assembled for influenza A and RSV. Interpretation: Non-SARS-CoV-2 respiratory viruses can be detected and sequenced from COVID-19 rapid antigen devices. Recovery of near full-length viral sequences from these devices provides a valuable opportunity to expand genomic surveillance programmes for public health monitoring of circulating respiratory viruses. Funding: Australian Government Medical Research Future Fund and Australian National Health and Medical Research Council.
MeSH term(s)	Humans ; COVID-19/diagnosis ; SARS-CoV-2/genetics ; Influenza, Human/diagnosis ; COVID-19 Testing ; Australia ; Metapneumovirus/genetics ; Paramyxoviridae Infections ; Respiratory Syncytial Virus, Human/genetics ; Whole Genome Sequencing
Language	English
Publishing date	2024-02-12
Publishing country	England
Document type	Journal Article
ISSN	2666-5247
ISSN (online)	2666-5247
DOI	10.1016/S2666-5247(23)00375-0
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Article ; Online: Mpox diagnostics: Review of current and emerging technologies.

Lim, Chuan Kok / Roberts, Jason / Moso, Michael / Liew, Kwee Chin / Taouk, Mona L / Williams, Eloise / Tran, Thomas / Steinig, Eike / Caly, Leon / Williamson, Deborah Ann

Journal of medical virology

2022 Volume 95, Issue 1, Page(s) e28429

Abstract: Mpox is a zoonotic disease caused by monkeypox virus (MPXV) from the Orthopoxvirus genus. Unprecedented transmission events have led to more than 70 000 cases reported worldwide by October 2022. The change in mpox epidemiology has raised concerns of its ... ...

Abstract	Mpox is a zoonotic disease caused by monkeypox virus (MPXV) from the Orthopoxvirus genus. Unprecedented transmission events have led to more than 70 000 cases reported worldwide by October 2022. The change in mpox epidemiology has raised concerns of its ability to establish endemicity beyond its traditional geographical locations. In this review, we discuss the current understanding of mpox virology and viral dynamics that are relevant to mpox diagnostics. A synopsis of the traditional and emerging laboratory technologies useful for MPXV detection and in guiding "elimination" strategies is outlined in this review. Importantly, development in MPXV genomics has rapidly advanced our understanding of the role of viral evolution and adaptation in the current outbreak.
MeSH term(s)	Animals ; Humans ; Mpox (monkeypox)/diagnosis ; Mpox (monkeypox)/epidemiology ; Monkeypox virus ; Zoonoses ; Orthopoxvirus ; Disease Outbreaks
Language	English
Publishing date	2022-12-09
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.28429
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