Novel SARS-CoV-2 Whole-genome sequencing technique using Reverse Complement PCR enables fast and accurate outbreak analysis (preprint)

Current transmission rates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still increasing and many countries are facing second waves of infections. Rapid SARS-CoV-2 whole genome sequencing (WGS) is often unavailable but could support public health organizations and hospitals in monitoring and determining transmission links. Here we report a novel reverse complement polymerase chain reaction (RC-PCR) technology for WGS of SARS-CoV-2. This technique is unique as it enables library preparation in a single PCR saving time, resources and enables high throughput screening. A total of 173 samples tested positive for SARS-CoV-2 between March and September 2020 were included. RC-PCR WGS applicability for outbreak analysis in public health service and hospital settings was tested on six predefined clusters containing samples of healthcare workers and patients. RC-PCR resulted in WGS data for 146 samples. It showed a genome coverage of up to 98,2% for samples with a maximum Ct value of 32. Three out of six suspected clusters were fully confirmed, while in other clusters four healthcare workers were not associated. Importantly, a previously unknown chain of transmission was confirmed in the public health service samples. These findings confirm the reliability and applicability of the RC-PCR technology for SARS-CoV-2 sequencing in outbreak analysis and surveillance.

Perceived Challenges of COVID-19 Infection Prevention and Control Preparedness: A Multinational Survey (preprint)

Objectives Implementation of effective infection prevention and control (IPC) measures is needed to support global capacity building to limit transmission of coronavirus disease 2019 (COVID-19) and mitigate its impact on health systems. We assessed the perceptions of healthcare workers on the current global IPC preparedness measures for COVID-19. Methods A cross-sectional survey using an electronic survey was circulated between February 26, 2020, and March 20, 2020, to IPC professionals during COVID-19 pandemic. The survey addressed the presence of COVID-19 guidelines as well as specific IPC preparedness activities in response to the outbreak. Findings In total, 339 IPC professionals spanning 63 countries in all 6 World Health Organization (WHO) regions, mostly from tertiary care centres participated. Of all participants, 66{middle dot}6% were aware of the existence of national guidelines to prevent COVID-19. A shortage of PPE supplies was reported by 48% (ranging from 64{middle dot}2% in low-income countries to 27{middle dot}4% in high-income countries); 41{middle dot}5% of respondents considered that the media had an impact on guideline development and 63{middle dot}6% believed that guidelines were based on maximum security rather than on evidence-based analyses. 58{middle dot}5% and 72{middle dot}7% of participants believed that healthcare facilities and community settings respectively were not sufficiently prepared. Conclusion Results revealed lack of guidelines and concerns over insufficient PPE supply in both high- and low-income countries. Our findings should alert national health authorities to ramp up the implementation of IPC measures and focus on long-term preparedness and readiness for future pandemics, likely requiring government funds rather than reliance on healthcare institutions.