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Authors: Judy Northill
Summary: A real-time assay to detect Aichivirus A (AiV-A) in human samples. It is based in the 3'UTR region and has been employed in our laboratory since 2007.

Proper citation: Judy Northill 2019. Aichivirus real-time RT-PCR 2007 method. protocols.io https://dx.doi.org/10.17504/protocols.io.z3tf8nn Copy   

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Authors: Ian Mackay, Judy Northill
Group: Public Health Virology, Forensic and Scientific Services
Summary: The protocol aims to specifically amplify Nipah viruses (NiV) and not other viruses.This is a modified version of a published assay. Modifications were to account for mismatches underneath oligo target sites.The assay targets the nucleoprotein (N) gene region and is designed as a qualitative test for investigating NiV infection of humans.

Proper citation: Ian Mackay, Judy Northill 2019. Nipah virus real-time RT-PCR (NiV-TM2018). protocols.io https://dx.doi.org/10.17504/protocols.io.rs5d6g6 Copy   

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Authors: Ian Mackay, Alyssa Pyke, Judy Northill
Group: Public Health Virology, Forensic and Scientific Services
Summary: The protocol aims explicitly to amplify RRV viruses and not other viruses.Alyssa Pyke designed the original assay which was published in 2011 (see below). Subsequently, Alyssa Pyke modified the reverse primer, and it is this most recent, revised version, described here.The assay targets the E2 gene region and is designed as a qualitative test for investigating RRV infection of humans and arthropods.

Proper citation: Ian Mackay, Alyssa Pyke, Judy Northill 2018. Ross River virus E2 TaqMan 2017 (RRV-E2-TM2017). protocols.io https://dx.doi.org/10.17504/protocols.io.rsyd6fw Copy   

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Authors: Judy Northill, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services
Summary: A real-time PCR to detect Orientia tsutsugamushi DNA. This method has been adapted from a publication by Jiang et al 2004, and  the oligonucleotides have been modified and a different PCR kit used.

Proper citation: Judy Northill, Ian Mackay 2018. Orientia tsutsugamushi real-time PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.rhfd33n Copy   

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Authors: Judy Northill, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services
Summary: A real-time PCR to broadly detect Rickettsia species DNA. This method has been adapted from a publication by Jiang et al 2012, and  the oligonucleotides have been modified and a different PCR kit used.

Proper citation: Judy Northill, Ian Mackay 2018. Rickettsia real-time PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.rg9d3z6 Copy   

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Authors: Ian Mackay, Judy Northill, Alyssa Pyke, Bruce Harrower
Group: Public Health Virology, Forensic and Scientific Services
Summary: This assay was designed and developed by Alyssa Pyke and Bruce Harrower at this laboratory aided by design software in use at the time. The assay specifically targets the haemagglutinin (HA) region of influenza A(H1)pdm09 virus strains and is designed as a qualitative screening test for human cases of infection, but not for infection due to other known influenza viruses. The assay aims to detect any circulating seasonal H1N1 influenza strains, not only influenza A(H1)pdm09 virus.

Proper citation: Ian Mackay, Judy Northill, Alyssa Pyke, Bruce Harrower 2018. Influenza A(H1)pdm09 virus TaqMan (SwFluH1) assay. protocols.io https://dx.doi.org/10.17504/protocols.io.rdhd236 Copy   

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Authors: Judy Northill, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services
Summary: Mayaro virus (MAYV) is an Alphavirus, transmitted by mosquitos in south and central America.This assay is designed to detect a portion of the nsP1 region of MAYV .

Proper citation: Judy Northill, Ian Mackay 2019. Mayaro virus real-time RT-PCR - 2016 method. protocols.io https://dx.doi.org/10.17504/protocols.io.2qxgdxn Copy   

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Authors: Judy Northill, Mitchell Finger, Michael Lyon, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services
Summary: A real-time RT-PCR using an MGB probe, this assay detects Japanese encephalitis virus (JEV) from human and mosquito samples.The assay targets the 3'UTR region of known JEV strains.

Proper citation: Judy Northill, Mitchell Finger, Michael Lyon, Ian Mackay 2017. Japanese encephalitis virus real-time RT-PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.kmscu6e Copy   

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Authors: Ian Mackay, Judy Northill
Group: Public Health Virology, Forensic and Scientific Services
Summary: This protocol was designed and developed at this laboratory. The assay specifically targets the 3' UTR region of DENV-4 strains and is designed as a qualitative screening test for human cases of DENV-4 infection, but not for infection due to other known DENVs.

Proper citation: Ian Mackay, Judy Northill 2018. Dengue virus type 4 (DENV-4) TaqMan (DENV4-TM2017) assay. protocols.io https://dx.doi.org/10.17504/protocols.io.n7pdhmn Copy   

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Authors: Ian Mackay, Judy Northill
Group: protocols.io Ambassadors, Public Health Virology, Forensic and Scientific Services
Summary: This protocol aims to amplify enterovirus (EV) D68 viruses and not other viruses.This protocol is modified from a previously published method cited below. Details of the modification are included in the method.The oligonucleotides target the 5'UTR noncoding region. This is a qualitative test for investigating EV-D68 infection of humans.The test has identified both the original EV-D68 strains and contemporary strains which has been confirmed by subgenomic sequencing of partial 5'UTR-VP2 and partial VP1 sequencing. Culture of the virus is not required as this assay is capable of detecting EV-D68 direct from extracted clinical samples.

Proper citation: Ian Mackay, Judy Northill 2018. Enterovirus (EV) D68 TaqMan 2018 (EV-D68-TM2018). protocols.io https://dx.doi.org/10.17504/protocols.io.vche2t6 Copy   

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Authors: Judy Northill, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community
Summary: A nested RT-PCR targeting the RdRp region of the sub-genus Sarbecovirus. The primers are modified from the pan-coronavirus RT-PCR published by Hu et al. 2017 to be more specific to SARS-CoV-2.Assay may be used in resource poor settings where real-time cyclers are not available.Sanger sequencing can be used to confirm SARS-CoV-2 where WGS is not available or where WGS fails due to poor quality sample.

Proper citation: Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.bcmpiu5n Copy   

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Authors: Mitchell Finger, Michael Lyon, Judy Northill, Ian Mackay
Summary: This previously unpublished protocol aims to amplify genotype A measles virus (MeV) strains but not non-mealses viruses.Mitchell Finger and Michael Lyon developed this in-house test in 2010.The assay targets the intergenic region between the M (matrix) and F (fusion) genes, designed as a qualitative test for investigating measles vaccine virus (MVV) strains.Numbering indicates the oligonucleotide location on the sequence with MeV strain Edmonston (Moraten vaccine), complete genome, GenBank accession number AF266287.

Proper citation: Mitchell Finger, Michael Lyon, Judy Northill, Ian Mackay 2019. Measles Vaccine Virus Taqman-MGB. protocols.io https://dx.doi.org/10.17504/protocols.io.2qugdww Copy   

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Authors: Judy Northill, Russell Simmons, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services
Summary: A real-time PCR method for the detection of Molluscum contagiosum virus from human samples. This assay targets the MC021L gene and detects both subtype 1 and 2 of the virus.

Proper citation: Judy Northill, Russell Simmons, Ian Mackay 2017. Molluscum contagiosum virus real-time PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.kmtcu6n Copy   

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Authors: Michael Lyon, Judy Northill, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services
Summary: This was a past assay that we no longer in use. For our favoured Measles TaqMan test, please refer to the MeV N TaqMan protocol.The protocol aims to amplify measles virus (MeV) strains and not other viruses.Michael Lyon designed the original version of this unpublished in-house assay in 1999. It was superseded in 2003 but occassionally brought out as needed for troubelshooting. The superseding test was a first generation MGB-TaqMan protocol called Measles MGB TaqMan FAST.The assay targets the fusion (F) gene region and is designed as a qualitative test for investigating MeV infection of humans.

Proper citation: Michael Lyon, Judy Northill, Ian Mackay 2018. Measles virus fusion (F) gene TaqMan (no longer in regular use; see Guidelines). protocols.io https://dx.doi.org/10.17504/protocols.io.rs7d6hn Copy   

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Authors: Ian Mackay, Ina Smith, Judy Northill
Group: Public Health Virology, Forensic and Scientific Services
Summary: The protocol aims explicitly to amplify BFV viruses and not other viruses. The assay targets the E2 gene region and is designed as a qualitative test for investigating BFV infection of humans and arthropods.

Proper citation: Ian Mackay, Ina Smith, Judy Northill 2018. Barmah Forest virus TaqMan 2017 (BFV-TM2017). protocols.io https://dx.doi.org/10.17504/protocols.io.rswd6fe Copy   

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Authors: Ian Mackay, Judy Northill
Group: Public Health Virology, Forensic and Scientific Services
Summary: This protocol was designed and developed at this laboratory. The protocol specifically aims to amplify strains of Influenza B VICTORIA virus lineage and not strains of the YAMAGATA virus lineage or other virus species. The assay targets the haemagglutinin (HA) region and is designed as a qualitative lineage-typing test for human cases of seasonal influenza virus type B infections. FluB-VICT-TM2018 is ideally used alongside its companion protocol, 'Influenza B virus YAMAGATA lineage TaqMan 2018' (FluB-YAMA-TM2018), which aims to target influenza B virus YAMAGATA lineage strains exclusively. The two assays perform best as UNIPLEX protocols; a drop in sensitivity was observed when combined in a DUPLEX format.

Proper citation: Ian Mackay, Judy Northill 2018. Influenza B virus VICTORIA lineage TaqMan 2018 / FluB-VICT-TM2018. protocols.io https://dx.doi.org/10.17504/protocols.io.reqd3dw Copy   

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Authors: Judy Northill, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community
Summary: A real-time RT-PCR designed to amplify a portion of the ORF1ab gene of sequences from the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)The probe and primers were published by the China CDC and are now included in the WHO in-house assay document.This test has been modified for use with our standard reagents and instrumentation.This test has identified clinical positive cases of coronavirus disease 2019 (COVID-19).

Proper citation: Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR CCDC-ORF1ab 2020. protocols.io https://dx.doi.org/10.17504/protocols.io.bgtnjwme Copy   

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Authors: Judy Northill, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services
Summary: A real-time PCR for the detection of Coxiella burnetii DNA targeting the IS1111a gene. The assay is based on a published method by Banazis et al 2010,  using a different PCR kit. The oligonucleitide sequences have not been modified however the concentration have been optimised. This method is used for testing DNA from human blood and tissue samples.

Proper citation: Judy Northill, Ian Mackay 2018. Coxiella burnetii real-time PCR - IS1111a method (Q fever). protocols.io https://dx.doi.org/10.17504/protocols.io.rhhd336 Copy   

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Authors: Greg A Smith, Alyssa Pyke, Judy Northill, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services
Summary: This protocol was designed and developed at this laboratory by Greg A. Smith and colleagues for Public Helath Virology, Queensland's Department of Health, prior to his departure. It has not been previously published. The protocol aims explicitly to amplify DENV-2 viruses and not other dengue viruses. The assay targets the membrane glycoprotein precursor region and is designed as a qualitative test for investigating suspected human cases of DENV-2 infection. This assay has been superseded by the Dengue virus type 2 (DENV-2) MGB TaqMan (DENV2-2016MGB) assay.

Proper citation: Greg A Smith, Alyssa Pyke, Judy Northill, Ian Mackay 2018. Dengue virus type 2 (DENV-2) prMG-Multiplex TaqMan assay (no longer in use; see Guidelines). protocols.io https://dx.doi.org/10.17504/protocols.io.rkzd4x6 Copy   

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Authors: Judy Northill, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services
Summary: A real-time PCR for Parapoxvirus targeting the DNA polymerase. It is used to screen human samples where Parapoxvirus is suspected.This protocol is based on the published RVSS assay by Das et al 2017. Oligonucleotides have been modified and a different PCR kit is used.

Proper citation: Judy Northill, Ian Mackay 2018. Parapoxvirus real-time PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.n38dgrw Copy   

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