Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia.

Genetically distinct variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged since the start of the COVID-19 pandemic. Over this period, we developed a rapid platform (R-20) for viral isolation and characterization using primary remnant diagnostic swabs. This, combined with quarantine testing and genomics surveillance, enabled the rapid isolation and characterization of all major SARS-CoV-2 variants circulating in Australia in 2021. Our platform facilitated viral variant isolation, rapid resolution of variant fitness using nasopharyngeal swabs and ranking of evasion of neutralizing antibodies. In late 2021, variant of concern Omicron (B1.1.529) emerged. Using our platform, we detected and characterized SARS-CoV-2 VOC Omicron. We show that Omicron effectively evades neutralization antibodies and has a different entry route that is TMPRSS2-independent. Our low-cost platform is available to all and can detect all variants of SARS-CoV-2 studied so far, with the main limitation being that our platform still requires appropriate biocontainment.

Lymphocyte cell population as a potential hematological index for early diagnosis of COVID-19

The pandemic diseases caused by SARS-CoV-2 are now threatening human health and survival. Early diagnosis and isolation of mild or asymptomatic COVID-19 patients is important to control the spread of SARS-CoV-2. In this study, we investigate the potential clinical utility of lymphocyte CPD for early diagnosis of COVID-19. To investigate the potential of lymphocyte cell population data (lymphocyte CPD) for use in early diagnosis of coronavirus disease 2019 (COVID-19). Lymphocyte CPD of healthy control (n=51), common cold patients (n=49) and mild COVID-19 patients (n=126) were generated using hematology analyzer. The parameters were subjected to sensitivity and specificity analysis to determine their suitability as biomarkers for early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Normality analysis showed that lymphocyte CPD followed a normal distribution. There were no significant differences in white blood cells (WBC) and lymphocyte (LY#) counts as well as the neutrophil-to-lymphocyte ratio (NLR) among the groups (p > 0.05). Lymphocyte volume standard deviation (LV-SD), lymphocyte conductivity standard deviation (LC-SD) and lymphocyte light scatter standard deviation (LS-SD) were significantly higher in the COVID-19 group than in common cold and control groups (p < 0.05). The corresponding mean lymphocyte light scattering (MLS) was significantly reduced in the COVID-19 group, relative to the common cold group, but was significantly increased, when compared with the control group (p < 0.05). Moreover, there was no significant difference in mean lymphocyte volume (MLV) between the COVID-19 group and the common cold or control group (p > 0.05), but it was significantly higher in the common cold group than in the control group (p < 0.05). At a cutoff value 16.38, LS-SD was more sensitive and specific than other lymphocyte CPD parameters. At a cutoff value 11.89, LC-SD achieved 84.4% sensitivity, 87.5% specificity, and an area under the curve (AUC) of 0.888. However, at a cutoff value 15.95, LS-SD reached 81.3% sensitivity, 75% specificity and an AUC of 0.876. These results suggest that lymphocyte CPD parameters have great diagnostic potential for SARS-CoV-2 infection and can be used for early diagnosis of the disease.