Ian M Mackay

The University of Queensland | UQ

Objective To explore the contribution of environmental in the unusual pattern of influenza activity observed in Brisbane, Australia during the summer of 2018-2019. Methods Distributed lag nonlinear models (DLNMs) were used to estimate the effect of environmental factors on weekly influenza incidence in Brisbane. Next generation sequencing was then...

We briefly describe a method to inoculate a susceptible cell line with a human patient sample in order to culture the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease, COVID-19. Clinical samples including nasopharyngeal swabs and aspirates were inoculated onto confluent monolayers of African green monke...

Purpose: Australia was officially recognised as having eliminated endemic measles transmission in 2014. Maintaining laboratory support for surveillance of vaccine-preventable diseases, such as measles, is an essential component of reaching and maintaining transmission-free status. Methodology: Real-time and conventional PCR-based tools were used...

This is my preferred, previously published [Ref 1], rhinovirus (RV) and enterovirus (EV) genotypingassay when seeking to identify the genotype of a respiratory picornavirus detected in a clinical sample extract. It is employed after use of a screeningreal-timeRT-PCR has identified a respiratory picornavirus. I have not confirmedthat it can detectev...

Purpose: Rhinoviruses (RVs) occur more frequently than other viruses and more often in people displaying symptoms than in those without. We sought to estimate the spectrum of RV diversity, RV species seasonality and to analyse RV involvement in respiratory virus co-detections. Methodology: A convenience collection of 1179 airway sample extracts...

This real-time TaqMan-MGB RT-PCR protocol aimed to amplify measles virus (MeV) strains and not other viruses. Michael Lyon and Mitchell Finger designed the assay in 2009 using Primer Express software. The method was later published by Greg Smith in 2010 (see below). The assay targets the fusion (F) gene region and is designed as a qualitative test...

The authors wish to make the following correction to Table 1 of this paper [...]

This test is a modification to the World Health Organization's influenza A H3 TaqMan documented in 'WHO information for molecular diagnosis of influenza virus - update 1' (see file below). New primers were added and the WHO primers discarded. The test targets the hemagglutinin (HA) gene.

Background: Malaria is the most important vector-borne disease in the world. Epidemiological and ecological studies of malaria traditionally utilize detection of Plasmodium sporozoites in whole mosquitoes or salivary glands by microscopy or serological or molecular assays. However, these methods are labor-intensive, and can over- or underestimate...

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 .

This real-time TaqMan-MGB RT-PCR protocol aimed to amplify measles virus (MeV) strains and not other viruses. Michael Lyon and Mitchell Finger designed the assay in 2009 using Primer Express software. The method was later published by Greg Smith in 2010 (see below). The assay targets the fusion (F) gene region and is designed as a qualitative test...

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 (M...

This assay is a modification to the World Health Organization's influenza A H3 TaqMan documented in 'WHO information for molecular diagnosis of influenza virus - update 1' (see file below). New primers were added and the WHO primers discarded.

Measles vaccines have been in use since the 1960s with excellent safety and effectiveness profiles. Limited data are available on detection of measles vaccine virus (MeVV) RNA in human subjects following vaccination. Available evidence suggests MeVV RNA can be identified up to 14 days after vaccination, with detection beyond this rare. In routine d...

Australia was officially recognised as having eliminated endemic measles circulation in 2014. Maintaining laboratory support for surveillance of vaccine-preventable diseases such as measles, is an essential component of reaching and maintaining circulation-free status. Between 2010 and 2017 over 13,700 specimens were tested in our laboratory by rea...

A real-time assay for the detection of Rubella virus RNA from clinical samples. This assay was modified from a published method with oligonucleotides updated, a different kit used, and cycling times adjusted accordingly.

Acute lower respiratory infection (ALRI) is a major cause of hospitalization for Indigenous children in remote regions of Australia. The associated microbiology remains unclear. Our aim was to determine whether the microbes present in the nasopharynx before an ALRI were associated with its onset. A retrospective case-control/crossover study among I...

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 (M...

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.

This real-time TaqMan-MGB RT-PCR protocol aimed to amplify measles virus (MeV) strains and not other viruses. Michael Lyon and Mitchell Finger designed the assay in 2009 using Primer Express software. The method was later published by Greg Smith in 2010 (see below). The assay targets the fusion (F) gene region and is designed as a qualitative test...

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 ou...

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 (M...

A real-time RT-PCR targeting the 5' untranslated region of Yellow fever virus. This protocol was designed and developed at this laboratory.

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.

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...

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.

Reference laboratories are vital for disease control and interpreting the complexities and impact of emerging pathogens. The role of these centralized facilities extends beyond routine screening capabilities to provide rapid, specific, and accurate diagnoses, advanced data analysis, consultation services, and sophisticated disease surveillance and...

This protocol was developed at this laboratory but had not been previously published. The protocol aims explicitly to amplify hepatitis A virus (HAV) strains and not other virus species. The assay targets the 5' untranslated region and is designed as a qualitative test for investigating suspected human cases of HAV infection.

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 prec...

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.

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.

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.

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 i...

This protocol was designed and developed at this laboratory. The protocol specifically aims to amplify strains of Influenza B YAMAGATA virus lineage and not strains of the VICTORIA 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 i...

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 i...

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 k...

This protocol was designed and developed at this laboratory and incorporates a previously published oligoprobe (see below). The protocol specifically aims to amplify DENV02 viruses and not other dengue viruses. The assay targets the capsid region and is designed as a qualitative test for investigating suspected human cases of DENV-2 infections. Thi...

Rhinoviruses (RVs) occur more frequently than other viruses and more often in people displaying symptoms than in those without. RVs exacerbate chronic airway disease and confound the clinical diagnosis of influenza-like illness. We sought to estimate the spectrum of RV diversity, RV species seasonality and to breakdown RV involvement in respiratory...

Zika virus (ZIKV) has spread widely in the Pacific and recently throughout the Americas. Unless detected by RT-PCR, confirming an acute ZIKV infection can be challenging. We developed and validated a multiplexed flavivirus immunoglobulin M (IgM) microsphere immunoassay (flaviMIA) which can differentiate ZIKV-specific IgM from that due to other flav...

This is a very handy, previously published [Ref 1 and 2], rhinovirus (RV) screening and genotyping assay which I and many others have used on many sample extracts, mostly originating fromacutely ill paediatric patients, spanning well over a decade's worth of collection dates. I have not confirmedthat it can detectevery single RV genotype but I do k...

This is a very handy, previously published [Ref 1 and 2], rhinovirus (RV) screening and genotyping assay which I and many others have used on many sample extracts, mostly originating fromacutely ill paediatric patients, spanning well over a decade's worth of collection dates. I have not confirmedthat it can detectevery single RV genotype but I do k...

This is my preferred, previously published [Ref 1], rhinovirus (RV) and enterovirus (EV) genotypingassay when seeking to characterize the genotypes of respiratory picornavirus identified after use of a screeningreal-timeRT-PCR to test nucleic acid extracts fromclinicalsamples. I have not confirmedthat it can detectevery single RV genotype but I do...

This is a very handy, previously published [Ref 1 and 2], rhinovirus (RV) screening assay which I and many others have used on many sample extracts, mostly originating fromacutely ill paediatric patients, spanning well over a decade's worth of collection dates. I have not confirmedthat it can detectevery single RV genotype but I do know that it det...

The human coronaviruses (CoV) include HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1, some of which have been known for decades. The severe acute respiratory syndrome (SARS) CoV briefly emerged into the human population but was controlled. In 2012, another novel severely human pathogenic CoV—the Middle East Respiratory Syndrome (MERS)-CoV—was ident...

Background: Parechoviruses (HPeV) are endemic seasonal pathogens detected from the respiratory tract, gut, blood and central nervous system (CNS) of children and adults, sometimes in conjunction with a range of acute illnesses. HPeV CNS infection may lead to neurodevelopmental sequelae, especially following infection by HPeV-3, hence screening and...

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.

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.

Objectives In children with hospitalised and non-hospitalised asthma exacerbations, to: (a) describe the point prevalence of respiratory viruses/atypical bacteria using polymerase chain reaction (PCR) and; (b) evaluate the impact of respiratory viruses/atypical bacteria and atopy on acute severity and clinical recovery. Design This was a prospecti...

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.

Objectives To describe the point prevalence of respiratory viruses/atypical bacteria using PCR and evaluate the impact of respiratory viruses/atypical bacteria and atopy on acute severity and clinical recovery in children with hospitalised and non-hospitalised asthma exacerbations. Design This was a prospective study performed during 2009–2011. S...

The paediatric intensive care unit (PICU) provides care to critically ill neonates, infants and children. These patients are vulnerable and susceptible to the environment surrounding them, yet there is little information available on indoor air quality and factors affecting it within a PICU. To address this gap in knowledge we conducted continuous...

Parechoviruses (HPeV) are not new viruses and are found in the respiratory tract and central nervous system of children and adults in conjunction with a range of acute illnesses. During an Australian outbreak of HPeV in the summer of 2013, we performed PCR-based screening and genotyping to determine whether ill Queensland infants were infected by H...

Toscana virus (TOSV) is identified in sandflies, animals and humans around the Mediterranean Sea. TOSV has not been reported in Australia. During investigations of cerebrospinal fluid samples from patients with encephalitis, TOSV genetic sequences were identified in a traveller returning to Australia from Europe. TOSV should be considered, especial...

Mayaro virus (MAYV) is an emerging arthropod-borne virus (arbovirus). Infection by MAYV can produce Mayaro virus disease (MAYVD) which is usually a clinically diagnosed, acute, febrile illness associated with prolonged and painful joint inflammation and swelling. MAYVD may be clinically indistinguishable from dengue, chikungunya fever, malaria, rab...

Background: Within the last 10 years Zika virus (ZIKV) has caused unprecedented epidemics of human disease in the nations and territories of the western Pacific and South America, and continues to escalate in both endemic and non-endemic regions. We evaluated the vector competence of Australian mosquitoes for ZIKV to assess their potential role in...

A community-based birth cohort study collected weekly nasal swabs and recorded daily symptoms from 157 full-term infants. An average of 0.25 (95% CI: 0.18, 0.34) respiratory virus infections per neonatal period were detected. Human rhinoviruses of diverse subtypes dominated; almost 50% were asymptomatic and continued rhinovirus detections may signi...

Influenza infection manifests in a wide spectrum of severity, including symptomless pathogen carriers. We conducted a systematic review and meta-analysis of 55 studies to elucidate the proportional representation of these asymptomatic infected persons. We observed extensive heterogeneity among these studies. The prevalence of asymptomatic carriage...

The first known cases of Middle East respiratory syndrome (MERS), associated with infection by a novel coronavirus (CoV), occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia (KSA). Since then, MERS-CoV sequences have been found in a bat and in many drom...

Bronchiolitis is a major health burden in infants globally, particularly among Indigenous populations. It is unknown if 3 weeks of azithromycin improve clinical outcomes beyond the hospitalization period. In an international, double-blind randomized controlled trial, we determined if 3 weeks of azithromycin improved clinical outcomes in Indigenous...

Human parainfluenza virus 4 (HPIV-4) subtypes 4a and 4b are seldom sought during molecular diagnostic screening of respiratory samples from patients with influenza like illnesses (ILIs). Nonetheless, HPIV-4a and HPIV-4b are to be found in such cases, occasionally in the absence of another pathogen. Little is known about the spectrum of genetic vari...

In 2012 in Jordan, infection by a novel coronavirus caused the first known cases of Middle East respiratory syndrome (MERS). MERS-CoV sequences have since been found in a bat and the virus appears to be enzootic among dromedary camels across the Arabian Peninsula and in parts of Africa. The majority of human cases have occurred in the Kingdom of Sa...

Respiratory viral infections precipitate exacerbations of chronic respiratory diseases such as asthma and chronic obstructive pulmonary disease though similar data in non-cystic fibrosis (CF) bronchiectasis are missing. Our study aimed to determine the point prevalence of viruses associated with exacerbations and evaluate clinical and investigation...

Background: The role of human adenoviruses (HAdVs) in chronic respiratory disease pathogenesis is recognized. However, no studies have performed molecular sequencing of HAdVs from the lower airways of children with chronic endobronchial suppuration. We thus examined the major HAdV genotypes/species, and relationships to bacterial coinfection, in c...

Prior studies on protracted bacterial bronchitis (PBB) in children have been retrospective or based on small cohorts. As PBB shares common features with other paediatric conditions, further characterisation is needed to improve diagnostic accuracy amongst clinicians. In this study, we aim to further delineate the clinical and laboratory features of...

Objective: Bronchiolitis, one of the most common reasons for hospitalisation in young children, is particularly problematic in Indigenous children. Macrolides may be beneficial in settings where children have high rates of nasopharyngeal bacterial carriage and frequent prolonged illness. The aim of our double-blind placebo-controlled randomised tr...

The comparative yield of respiratory virus detection from nasopharyngeal aspirate (NPA) versus bronchoalveolar lavage (BAL) is uncertain. Furthermore, the significance of virus detection and its relationship to lower airway neutrophilic inflammation is poorly studied. To evaluate the sensitivity, specificity and predictive values of NPA for detecti...

We used data on age and sex for 136 laboratory confirmed human A(H7N9) cases reported as of 11 August 2013 to compare age-specific and sex-specific patterns of morbidity and mortality from the avian influenza A(H7N9) virus with those of the avian influenza A(H5N1) virus. Human A(H7N9) cases exhibit high degrees of age and sex bias: mortality is hea...

While the discovery of HRV-Cs is recent, there are no indications that they are new viruses, or that they are emerging in real-time. Genetically, HRV-Cs are most closely related to the members of HRV-A and HRV-B but even a small genetic difference can impart encompass significant changes to their clinical impact, complicated by a diverse human back...

Bronchiectasis unrelated to cystic fibrosis (CF) is being increasingly recognized in children and adults globally, both in resource-poor and in affluent countries. However, high-quality evidence to inform management is scarce. Oral amoxycillin-clavulanate is often the first antibiotic chosen for non-severe respiratory exacerbations, because of the...

Introduction Even in developed economies infectious diseases remain the most common cause of illness in early childhood. Our current understanding of the epidemiology of these infections is limited by reliance on data from decades ago performed using low-sensitivity laboratory methods, and recent studies reporting severe, hospital-managed disease....

Background Despite bronchiectasis being increasingly recognised as an important cause of chronic respiratory morbidity in both indigenous and non-indigenous settings globally, high quality evidence to inform management is scarce. It is assumed that antibiotics are efficacious for all bronchiectasis exacerbations, but not all practitioners agree. In...

Human rhinovirus (HRV) replication triggers exacerbation of asthma and causes most acute respiratory illnesses (ARIs), which may manifest as influenza-like illness. The recent assignment of 60 previously unknown HRV types to a third HRV species, Human rhinovirus C, raised questions about the prevalence of these picornavirus types in the community,...

Etiologic agents of genital ulcer disease include herpes simplex 1 and 2, Treponema pallidum pallidum, Haemophilus ducreyi, and Klebsiella granulomatis. The advent of PCR has allowed for more rapid and sensitive detection of microbial pathogens. In this protocol, we describe the simultaneous detection of these five pathogens and an internal control...

Acute respiratory illnesses (ARIs) with unconfirmed infectious aetiologies peak at different times of the year. Molecular diagnostic assays reduce the number of unconfirmed ARIs compared to serology- or culture-based techniques. Screening of 888 inpatient and outpatient respiratory specimens spanning late autumn through to early spring, 2004, ident...