An understanding of discordant SARS-CoV-2 test results: An examination of the data from a central Auckland laboratory

AIM: The diagnostic sensitivity of the SARS-CoV-2 real time reverse transcription polymerase chain reaction (RT-PCR) test has not been determined. This has led to a degree of uncertainty in the interpretation of results, particularly in patients tested repeatedly. The aim of this study was to explore the characteristics of patients who initially tested negative, and subsequently tested positive for SARS-CoV-2. METHOD(S): This retrospective observational study utilised data from the LabPlus Virology laboratory, Auckland City Hospital, to identify cases (hospital and community) with initial negative and subsequent positive SARS-CoV-2 RT-PCR results. Their clinical and laboratory characteristics were summarised. RESULT(S): From 1 February to 13 April a total of 20,089 samples were received for SARS-CoV-2 testing. Of 2,011 samples from patients with multiple tests, 25 samples were positive. Nine samples were from patients who initially tested negative then tested positive. Reasons for the initial negative test results, which were all from upper respiratory tract samples, included pre-symptomatic presentation or late presentation. All patients had significant risk factors and ongoing or evolving symptoms, which warranted repeat testing. CONCLUSION(S): Few patients had discordant test results for SARS-CoV-2 RT-PCR. For patients who have a significant risk factor and a negative test result, repeat testing should be performed. Copyright © 2020 New Zealand Medical Association. All rights reserved.

Age-related differences in SARS-CoV-2 testing in the Northern Region of New Zealand

AIM: There is concern the low incidence of coronavirus disease 2019 (COVID-19) in children reflects undertesting in this population. This study sought to describe the age-distribution of SARS-CoV-2 testing in the Northern Region of New Zealand. METHODS: A retrospective single-centre review of all SARS-CoV-2 tests performed at LabPLUS, Auckland City Hospital, between 12 February and 18 April 2020. RESULTS: A total of 22,333 tests were performed, with 313 (1.40%) positive results. The age-adjusted SARS-CoV-2 testing rate was three times higher in adults than in children. The overall proportion of positive tests was lower in children (0.86%) than adults (1.45%). However, within the paediatric population the proportion of tests positive differed significantly between those <10 years old (0.08%) and those 10-14 years old (2.6%). CONCLUSION: The lower proportion of tests positive in children <10 years of age suggests they are appropriately tested relative to their rates of disease. A large high school-associated cluster makes the higher proportion of tests positive in children 10-14 years old difficult to interpret. Older children may have a higher risk of infection and increasing testing in intermediate and high school aged children may be indicated. © 2020 New Zealand Medical Association. All rights reserved.

Sensitivity and potential utility of SARS-CoV-2 rapid antigen and nucleic acid amplification tests in the context of an elimination approach

AIM: To assess the sensitivity and potential utility of five RATs and the IDNow, Liat and Oxsed nucleic acid amplification tests (NAATs) in our population. METHOD: 39 retrospective and contrived SARS-CoV-2 positive samples were tested in parallel by standard RT-PCR and RAT. A second group of 44 samples was tested by standard RT-PCR, rapid RT-PCR and two isothermal NAAT assays. Limit of detection was compared at RT-PCR cycle thresholds for all assays. RESULTS: We found that the Cobas Liat RT-PCR had 100% concordance with conventional RT-PCR, whereas the sensitivity of other rapid NAAT assays was less at lower viral loads indicated by Cts >30 (p=0.042) and the RATs at Cts >25 (p <0.001). When applied to New Zealand testing scenarios, IDNow or Oxsed NAAT could miss up to 12% and RATs up to 44.3% of COVI D-19 cases compared with the RT-PCR currently used at our laboratory. CONCLUSION: We found that the POC Cobas Liat, a platform that delivers a sample answer in 20 minutes, demonstrated equivalent performance to standard RT-PCR. However, the RATs and isothermal NAAT assays demonstrated reduced sensitivity, limiting their utility in New Zealand's currently very low prevalence setting.

COVID-19 serology: use and interpretation in New Zealand

Serology is now a well-established diagnostic tool for the diagnosis of COVID-19 infections in New Zealand. Using local and international experience, we provide an overview of serological response to infection and vaccination as well as the use and interpretation of antibody tests in our setting. We also discuss the potential future role of post-vaccination serology testing as a correlate of immunity. We conclude that, given the pitfalls of testing, clinical microbiologist advice is necessary for interpretation of high-consequence cases.

An understanding of discordant SARS-CoV-2 test results: an examination of the data from a central Auckland laboratory

AIM: The diagnostic sensitivity of the SARS-CoV-2 real time reverse transcription polymerase chain reaction (RT-PCR) test has not been determined. This has led to a degree of uncertainty in the interpretation of results, particularly in patients tested repeatedly. The aim of this study was to explore the characteristics of patients who initially tested negative, and subsequently tested positive for SARS-CoV-2. METHODS: This retrospective observational study utilised data from the LabPlus Virology laboratory, Auckland City Hospital, to identify cases (hospital and community) with initial negative and subsequent positive SARS-CoV-2 RT-PCR results. Their clinical and laboratory characteristics were summarised. RESULTS: From 1 February to 13 April a total of 20,089 samples were received for SARS-CoV-2 testing. Of 2,011 samples from patients with multiple tests, 25 samples were positive. Nine samples were from patients who initially tested negative then tested positive. Reasons for the initial negative test results, which were all from upper respiratory tract samples, included pre-symptomatic presentation or late presentation. All patients had significant risk factors and ongoing or evolving symptoms, which warranted repeat testing. CONCLUSION: Few patients had discordant test results for SARS-CoV-2 RT-PCR. For patients who have a significant risk factor and a negative test result, repeat testing should be performed.

Age-related differences in SARS-CoV-2 testing in the Northern Region of New Zealand

AIM: There is concern the low incidence of coronavirus disease 2019 (COVID-19) in children reflects undertesting in this population. This study sought to describe the age-distribution of SARS-CoV-2 testing in the Northern Region of New Zealand. METHODS: A retrospective single-centre review of all SARS-CoV-2 tests performed at LabPLUS, Auckland City Hospital, between 12 February and 18 April 2020. RESULTS: A total of 22,333 tests were performed, with 313 (1.40%) positive results. The age-adjusted SARS-CoV-2 testing rate was three times higher in adults than in children. The overall proportion of positive tests was lower in children (0.86%) than adults (1.45%). However, within the paediatric population the proportion of tests positive differed significantly between those <10 years old (0.08%) and those 10-14 years old (2.6%). CONCLUSION: The lower proportion of tests positive in children <10 years of age suggests they are appropriately tested relative to their rates of disease. A large high school-associated cluster makes the higher proportion of tests positive in children 10-14 years old difficult to interpret. Older children may have a higher risk of infection and increasing testing in intermediate and high school aged children may be indicated.