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| Name | Authors | DOI | Group |
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Associated Publications |
RRIDs used | ||||||
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Japanese encephalitis virus real-time RT-PCR Resource Report Resource Website |
Judy Northill, Mitchell Finger, Michael Lyon, Ian Mackay | DOI:10.17504/protocols.io.r23d8gn | Public Health Virology, Forensic and Scientific Services | 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. | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | https://doi.org/10.1089/vbz.2013.1373 | 3 | 2018 | Judy Northill, Mitchell Finger, Michael Lyon, Ian Mackay 2018. Japanese encephalitis virus real-time RT-PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.r23d8gn | 2021-04-15 09:16:30 | ||
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR Resource Report Resource Website |
Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.bgz2jx8e | Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community | 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, though other coronaviruses may still be detected. Assay may be used in resource poor settings where real-time cyclers are not available.Sanger sequencing should be used to confirm SARS-CoV-2 where WGS is not available or where WGS fails due to poor quality sample. | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 3 | 2020 | 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.bgz2jx8e | 2021-04-15 09:16:57 | |||
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR E gene 2020 Resource Report Resource Website |
Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.bcv9iw96 | Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community | A real-time RT-PCR designed to amplify a portion of the envelope gene of sequences from the Betacoronavirus sub-genus Sarbecovirus.The probe and primers were published by Corman et al., and we have slightly modified the protocol, increasing the concentration of the reverse primer, using a different kit and different cycling conditions.This test has identified clinical positive cases of coronavirus disease 2019 (COVID-19). | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 1 | 2020 | Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR E gene 2020. protocols.io https://dx.doi.org/10.17504/protocols.io.bcv9iw96 | 2021-04-15 09:16:40 | |||
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR N gene 2020 (Wuhan-N; 2019-nCoV-related test) -NOT RECOMMENDED Resource Report Resource Website |
Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.bchwit7e | protocols.io Ambassadors, Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community | NOT RECOMMENDED FOR SCREENINGThe sensitivity of the assay has been found to be lower than expected and we no longer recommend it be used.We do recommend the ORF1ab assay (Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR ORF1ab 2020) or the E gene assay by Corman et al. (Protocol v2-1)A real-time RT-PCR to designed to detect SARS-CoV-2 and other related sarbecoviruses. Based on sequence MN908947 made available by Professor Yong-Zhen Zhang, Fudan University, Shanghai, China. The target region encodes the nucleocapsid (N).Not tested on wild-type virus (as of 25Jan2020), it is expected to be capable of detecting Wuhan virus, bat-like SARS and SARS virus (members of the subgenus Sarbecovirus).Limit of detection not yet determined.A single 1 mismatch at probe-binding site identified with the BetaCoV/USA/CA1/2020|EPI_ISL_406034 variant of SARS-CoV-2 (as of 29JAN2020).Probe is in the 3'-5' (reverse complement) direction.A real-time RT-PCR to designed to detect SARS-CoV-2 and other related sarbecoviruses. Based on sequence MN908947 made available by Professor Yong-Zhen Zhang, Fudan University, Shanghai, China. The target region encodes the nucleocapsid (N).Not tested on wild-type virus (as of 25Jan2020), it is expected to be capable of detecting Wuhan virus, bat-like SARS and SARS virus (members of the subgenus Sarbecovirus).Limit of detection not yet determined.A single 1 mismatch at probe-binding site identified with the BetaCoV/USA/CA1/2020|EPI_ISL_406034 variant of SARS-CoV-2 (as of 29JAN2020).Probe is in the 3'-5' (reverse complement) direction.Notes: Assay is optimised (as of 24Jan2020).This test has identified a clinical positive case of coronavirus disease (COVID-19) | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 4 | 2020 | Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR N gene 2020 (Wuhan-N; 2019-nCoV-related test) -NOT RECOMMENDED. protocols.io https://dx.doi.org/10.17504/protocols.io.bchwit7e | 2021-04-15 09:16:46 | |||
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Enterovirus (EV) A71 real-time RT-PCR (EV-A71-TM2018) Resource Report Resource Website |
Ian Mackay, Judy Northill | DOI:10.17504/protocols.io.xb3fiqn | Public Health Virology, Forensic and Scientific Services | This protocol aims to amplify enterovirus (EV) A71 viruses but not other viruses.This protocol was designed by us.The oligonucleotides target the 5'UTR noncoding region. This is a qualitative test for investigating EV-A71 infection of humans.The test has identified both historical EV-A71 strains and contemporary strains and has confirmed these using 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-A71 direct from extracted clinical samples. | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 2 | 2019 | Ian Mackay, Judy Northill 2019. Enterovirus (EV) A71 real-time RT-PCR (EV-A71-TM2018). protocols.io https://dx.doi.org/10.17504/protocols.io.xb3fiqn | 2021-04-15 09:17:05 | |||
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR Resource Report Resource Website |
Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.bdcpi2vn | Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community | 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. | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 2 | 2020 | 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.bdcpi2vn | 2021-04-15 09:17:04 | |||
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Human Parechovirus A real-time RT-PCR ["Nix assay"; 2008-2015] Resource Report Resource Website |
Ian Mackay | DOI:10.17504/protocols.io.k2jcycn | I and my team used this assay between 2008-2015; we dubbed it the "Nix assay". It targets the 5'UTR and employs quite degenerate oligos.In silico sequence alignments indicated the olignucleotides could theoretically detect aft least HPeV 1-7, 17 and 18.However during a period of assay comparison, another assay (see link below), the "Benschop assay" (J.Clin.Virol. 2008. 41(2):69-74), was found to produce more sigmoidal and higher curves and 1-5 cycle improvements to CT values when compared among the sample sampe extract set. | The University of Queensland | 1 | 2017 | Ian Mackay 2017. Human Parechovirus A real-time RT-PCR ["Nix assay"; 2008-2015]. protocols.io https://dx.doi.org/10.17504/protocols.io.k2jcycn | 2021-04-15 09:17:08 |
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