Impact of the COVID-19 related border restrictions on influenza and other common respiratory viral infections in New Zealand.

BACKGROUND: New Zealand's (NZ) complete absence of community transmission of influenza and respiratory syncytial virus (RSV) after May 2020, likely due to COVID-19 elimination measures, provided a rare opportunity to assess the impact of border restrictions on common respiratory viral infections over the ensuing 2 years. METHODS: We collected the data from multiple surveillance systems, including hospital-based severe acute respiratory infection surveillance, SHIVERS-II, -III and -IV community cohorts for acute respiratory infection (ARI) surveillance, HealthStat sentinel general practice (GP) based influenza-like illness surveillance and SHIVERS-V sentinel GP-based ARI surveillance, SHIVERS-V traveller ARI surveillance and laboratory-based surveillance. We described the data on influenza, RSV and other respiratory viral infections in NZ before, during and after various stages of the COVID related border restrictions. RESULTS: We observed that border closure to most people, and mandatory government-managed isolation and quarantine on arrival for those allowed to enter, appeared to be effective in keeping influenza and RSV infections out of the NZ community. Border restrictions did not affect community transmission of other respiratory viruses such as rhinovirus and parainfluenza virus type-1. Partial border relaxations through quarantine-free travel with Australia and other countries were quickly followed by importation of RSV in 2021 and influenza in 2022. CONCLUSION: Our findings inform future pandemic preparedness and strategies to model and manage the impact of influenza and other respiratory viral threats.

Development of real-time RT-PCR assays to detect measles virus on the Hologic Panther Fusion® System.

BACKGROUND: In 2019, Aotearoa New Zealand (NZ) experienced its worst measles outbreak since 1997. Due to declining childhood vaccination rates since the beginning of the SARS-CoV-2 pandemic, NZ is at serious risk of another major measles outbreak. Our laboratory provides diagnostic services to NZ's Southern region. In 2019 the Southern region experienced the greatest number of cases outside of Auckland and Northland, however we did not have a validated measles PCR assay in our laboratory. OBJECTIVES: We sought to develop reverse transcription real-time polymerase chain reaction (RT-PCR) assays for measles on the Hologic Panther Fusion® System by utilising its open access function. STUDY DESIGN: Previously published real-time RT-PCR assays were modified and optimised to detect wild-type measles virus (LDT-Mea), and the vaccine strain of measles virus (LDT-MeaVacA), on the Hologic Panther Fusion® System. The assays were clinically validated. RESULTS: The LDT-Mea assay has a limit of detection (LoD) of 0.1 CCID50, while the LDT-MeaVacA assay is less sensitive with a LoD of 1 CCID50. Using 27 samples, the clinical sensitivity and specificity was 100% for both assays. Other common respiratory viruses were found not to cross-react with either the LDT-Mea or LDT-MeaVacA assays. CONCLUSION: We have successfully adapted and validated for diagnostic use on the Hologic Panther Fusion® System previously published assays to detect wild-type and vaccine strains of the measles virus. The implementation of measles testing on this system will greatly improve the turn-around time for measles testing, and better support the measles public health response, for our region.

A comparison of the performance of saliva and nasopharyngeal nucleic acid amplification testing for the detection of SARS-CoV-2 in New Zealand.

AIM: To compare detection of SARS-CoV-2 from paired nasopharyngeal swabs (NPS) and saliva using molecular methods in common use for testing swabs in New Zealand. METHOD: Samples from individuals testing positive for SARS-CoV-2 in Auckland, Wellington and Dunedin were tested at the local laboratories using methods previously established for these sample types. RESULTS: One hundred and ninety-six paired samples from unique individuals were tested, with 46 (23%) positive from either sample type, of which 43/46 (93%) tested positive from NPS, and 42/46 (91%) from saliva, indicating no significant difference in performance between sample types (p=0.69). The average Δ Ct between saliva and nasopharyngeal swabs overall across the sample set was 0.22 cycles, indicating excellent concordance; however, the difference between NPS and saliva collected from the same individual was quite variable with up to 19 cycles difference between the sample types. CONCLUSION: We found that saliva is an equivalent sample type to nasopharyngeal swab for the detection of SARS-CoV-2 in our laboratories using multiple assay combinations and is suitable for use as a diagnostic and surveillance test for selected groups of individuals.

The design, validation and clinical verification of an in-house qualitative PCR to detect Yersinia enterocolitica and Yersinia pseudotuberculosis in faeces.

Yersiniosis is a zoonotic foodborne infection of public health significance. The aim of this study was to design and validate a simple, accurate and cost-effective polymerase chain reaction (PCR) to detect pathogenic Yersinia spp. in faecal samples. An intercalating dye (EvaGreen)-based real-time multiplex PCR assay was designed to detect yadA, ystB and inv by melt curve analysis, allowing undifferentiated detection of all Yersinia enterocolitica biotypes, including biotype 1A, and Yersinia pseudotuberculosis. The assay was validated using cultured bacteria and clinical samples. A total of 107 positive and 51 negative samples were tested. The sensitivity and specificity was 98% and 100%. The limit of detection was 104-105 CFU/g faeces. A total of 605 samples (9 positive) were tested in the clinical verification with an accuracy and negative predictive value of 99% [95% confidence interval (CI) 97.9-99.6%] and 99.8% (95% CI 97.9-99.6%), respectively. This is an accurate, simple and cost-effective assay for the detection of pathogenic Yersinia spp.

Rothia aeria as a cause of sepsis in a native joint.

Rothia aeria is a recently described Gram-positive rod from the family Micrococcaceae. An elderly woman with rheumatoid arthritis and dental abscesses who was undergoing immunosuppression had R. aeria isolated from synovial fluid. This report characterizes this rare organism and contributes to the literature on its pathogenicity and likely oral source.

Hospitalizations for pandemic (H1N1) 2009 among Maori and Pacific Islanders, New Zealand.

Community transmission of influenza A pandemic (H1N1) 2009 was followed by high rates of hospital admissions in the Wellington region of New Zealand, particularly among Maori and Pacific Islanders. These findings may help health authorities anticipate the effects of pandemic (H1N1) 2009 in other communities.