Household Transmission of SARS-CoV-2 along the Evolution of Pandemic (preprint)

Over the past three years, we have gained some understanding of the transmission mechanisms of COVID-19. One of the key findings that experts have agreed on is that household transmission is an important pathway for the pandemic. However, most studies on the transmission patterns of COVID-19 focus on the community transmission only, while the equally important study on household transmission has lagged behind. We developed a stochastic dynamic model motivated by the cluster growth algorithm in Erdös–Rényi Random Graph to differentiate the COVID-19 transmission within households from that in the community by noting only a small fraction of the total susceptible population, replenished dynamically by the community transmission events, are indeed vulnerable to household transmission. Thus the model allowed us to the role and characteristics of household transmission within the full framework of virus transmission, beyond the intrinsic characteristics of household transmission. It was then applied to a comprehensive individual-level pandemic dataset collected in Yichang, China. Our findings showed that household transmission accounted for 25.1% and 38.5% of total infections before and during the lockdown, respectively, and that 80.9% of infections were unavoidable. Our model suggests that household-level contact tracing could have reduced the number of infections by over 50% and advanced the clearance date of active infection by 72 days. This model can be used to fit COVID-19 data outside Yichang or other infectious diseases, though modifications might be needed.

The incidence of positive bloodstream and urine cultures in five Australian hospitals during the COVID-19 pandemic (preprint)

Background The COVID-19 pandemic has had a significant impact on healthcare including increased awareness of infection prevention and control (IPC). The aim of this study was to explore if the heightened awareness of IPC measures implemented in response to the pandemic influenced the rates of healthcare associated infections (HAI) using positive bloodstream and urine cultures as a proxy measure.Methods A 3 year retrospective review of laboratory data from 5 hospitals (4 acute public, 1 private) from two states in Australia was undertaken. Monthly positive bloodstream culture data and urinary culture data were collected from January 2017 to March 2021. Occupied bed days (OBDs) were used to generate monthly HAI incidence per 10,000 OBDs. An interrupted time series analysis was undertaken to compare incidence pre and post February 2020 (the pre COVID-19 cohort and the COVID-19 cohort respectively). A HAI was assumed if positive cultures were obtained 48 hours after admission and met other criteria.Results A total of 1,988 bloodstream and 7,697 urine positive cultures were identified. The unadjusted incident rate was 25.5 /10,000 OBDs in the pre-COVID-19 cohort, and 25.1/10,000 OBDs in the COVID-19 cohort. The overall rate of HAI aggregated for all sites did not differ significantly between the two periods. The two hospitals in one state which experienced an earlier and larger outbreak demonstrated a significant downward trend in the COVID-19 cohort (p = 0.011).Conclusion These mixed findings reflect the uncertainty of the effect the pandemic has had on HAI’s. Factors to consider in this analysis include local epidemiology, differences between public and private sector facilities, changes in patient populations and profiles between hospitals, and timing of enhanced IPC interventions. Future studies which factor in these differences may provide further insight on the effect of COVID-19 on HAIs.

Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia (preprint)

We report on an analysis of Australian COVID-19 case data to estimate the impact of TTIQ systems on SARS-CoV-2 transmission in 2020-21. We estimate that in a low prevalence period in the state of New South Wales (tens of cases per day), TTIQ contributed to a 54% reduction in transmission. In a higher prevalence period in the state of Victoria (hundreds of cases per day), TTIQ contributed to a 42% reduction in transmission. Our results also suggest that case-initiated contact tracing can support timely quarantine in times of system stress. Contact tracing systems for COVID-19 in Australia were highly effective and adaptable in supporting the national suppression strategy through 2020 and 2021.

COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting (preprint)

Since the emergence of SARS-CoV-2 in 2019 through to mid-2021, much of the Australian population lived in a COVID-19 free environment. This followed the broadly successful implementation of a strong suppression strategy, including international border closures. With the availability of COVID-19 vaccines in early 2021, the national government sought to transition from a state of minimal incidence and strong suppression activities to one of high vaccine coverage and reduced restrictions but with still-manageable transmission. This transition is articulated in the national ``re-opening" plan released in July 2021. Here we report on the dynamic modelling study that directly informed policies within the national re-opening plan including the identification of priority age groups for vaccination, target vaccine coverage thresholds and the anticipated requirements for continued public health measures --- assuming circulation of the Delta SARS-CoV-2 variant. Our findings demonstrated that adult vaccine coverage needed to be at least 70% to minimise public health and clinical impacts following the establishment of community transmission. They also supported the need for continued application of test-trace-isolate-quarantine and social measures during the vaccine roll-out phase and beyond.