Microbiology & Immunology - Research Publications

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Author: Purcell, Damian × Author: Williamson, Deborah × Start date: 2020 × Type: Preprint ×

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    Evaluation of serological tests for SARS-CoV-2: Implications for serology testing in a low-prevalence setting
    Bond, K ; Nicholson, S ; Ming Lim, S ; Karapanagiotidis, T ; Williams, E ; Johnson, D ; Hoang, T ; Sia, C ; Purcell, D ; R Lewin, S ; Catton, M ; P Howden, B ; A Williamson, D ( 2020)

    Background

    Robust serological assays are essential for long-term control of the COVID-19 pandemic. Many recently released point-of-care (PoCT) serological assays have been distributed with little pre-market validation.

    Methods

    Performance characteristics for five PoCT lateral flow devices approved for use in Australia were compared to a commercial enzyme immunoassay (ELISA) and a recently described novel surrogate virus neutralisation test (sVNT).

    Results

    Sensitivities for PoCT ranged from 51.8% (95% CI 43.1 to 60.4%) to 67.9% (95% CI 59.4–75.6%), and specificities from 95.6% (95% CI 89.2–98.8%) to 100.0% (95% CI 96.1–100.0%). Overall ELISA sensitivity for either IgA or IgG detection was 67.9% (95% CI 59.4–75.6), increasing to 93.8% (95% CI 85.0–98.3%) for samples > 14 days post symptom onset. Overall, sVNT sensitivity was 60.9% (95% CI 53.2–68.4%), rising to 91.2%% (95% CI 81.8–96.7%) for samples collected > 14 days post-symptom onset, with a specificity 94.4% (95% CI 89.2–97.5%),

    Conclusion

    Performance characteristics for COVID-19 serological assays were generally lower than those reported by manufacturers. Timing of specimen collection relative to onset of illness or infection is crucial in the reporting of performance characteristics for COVID-19 serological assays. The optimal algorithm for implementing serological testing for COVID-19 remains to be determined, particularly in low-prevalence settings.
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    Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection.
    Chang, JJ-Y ; Rawlinson, D ; Pitt, M ; Taiaroa, G ; Gleeson, J ; Zhou, C ; Mordant, F ; Paoli-Iseppi, RD ; Caly, L ; Purcell, DFJ ; Stinear, T ; Londrigan, S ; Clark, M ; Williamson, D ; Subbarao, K ; Coin, LJM ( 2020-12-22)
    SARS-CoV-2 uses subgenomic (sg)RNA to produce viral proteins for replication and immune evasion. We applied long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA was upregulated earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of ORF1ab containing nsp1 joined to ORF10 and 3’UTR was upregulated at 48 hours post infection in human cell lines. We identified double-junction sgRNA containing both TRS-dependent and independent junctions. We found multiple sites at which the SARS-CoV-2 genome is consistently more modified than sgRNA, and that sgRNA modifications are stable across transcript clusters, host cells and time since infection. Our work highlights the dynamic nature of the SARS-CoV-2 transcriptome during its replication cycle. Our results are available via an interactive web-app at http://coinlab.mdhs.unimelb.edu.au/ .