ABSTRACT
BackgroundCurrent 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 the use of reverse complement polymerase chain reaction (RC-PCR), a novel technology for WGS of SARS-CoV-2 enabling library preparation in a single PCR saving time, resources and enables high throughput screening. Additionally, we show SARS-CoV-2 diversity and possible transmission within the Radboud university medical center (Radboudumc) during September 2020 using RC-PCR WGS. MethodsA total of 173 samples tested positive for SARS-CoV-2 between March and September 2020 were selected for whole-genome sequencing. Ct values of the samples ranged from 16 to 42. They were collected from 83 healthcare workers and three patients at the Radboudumc, in addition to 64 people living in the area around the hospital and tested by the local health services. For validation purposes, nineteen of the included samples were previously sequenced using Oxford Nanopore Technologies and compared to RC-PCR WGS results. The applicability of RC-PCR WGS in outbreak analysis for public health service and hospitals was tested on six suspected clusters containing samples of healthcare workers and patients with an epidemiological link. FindingsRC-PCR resulted in sequencing data for 146 samples. It showed a genome coverage of up to 98,2% for samples with a maximum Ct value of 32. Comparison to Oxford Nanopore technologies gives a near-perfect agreement on 95% of the samples (18 out of 19). Three out of six clusters with a suspected epidemiological link were fully confirmed, in the others, four healthcare workers were not associated. In the public health service samples, a previously unknown chain of transmission was confirmed. Significance statementSAR-CoV-2 whole-genome sequencing using RC-PCR is a reliable technique and applicable for use in outbreak analysis and surveillance. Its ease of use, high-trough screening capacity and wide applicability makes it a valuable addition or replacement during this ongoing SARS-CoV-2 pandemic. FundingNone Research in contextO_ST_ABSEvidence before this studyC_ST_ABSAt present whole genome sequencing techniques for SARS-CoV-2 have a large turnover time and are not widely available. Only a few laboratories are currently able to perform large scale SARS-CoV-2 sequencing. This restricts the use of sequencing to aid hospital and community infection prevention. Added value of this studyHere we present clinical and technical data on a novel Whole Genome Sequencing technology, implementing reverse-complement PCR. It is able to obtain high genome coverage of SARS-CoV-2 and confirm and exclude epidemiological links in 173 healthcare workers and patients. The RC-PCR technology simplifies the workflow thereby reducing hands on time. It combines targeted PCR and sequence library construction in a single PCR, which normally takes several steps. Additionally, this technology can be used in concordance with the widely available range of Illumina sequencers. Implications of all the available evidenceRC-PCR whole genome sequencing technology enables rapid and targeted surveillance and response to an ongoing outbreak that has great impact on public health and society. Increased use of sequencing technologies in local laboratories can help prevent increase of SARS-CoV-2 spreading by better understanding modes of transmission.
ABSTRACT
ObjectivesImplementation 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. MethodsA 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. FindingsIn 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. ConclusionResults 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.
ABSTRACT
The public health response to coronavirus disease 2019 (COVID-19) in China has illustrated that it is possible to contain COVID-19 if governments focus on tried and tested public health outbreak responses.1,2 Isolation, quarantine, social distancing, and community containment measures were rapidly implemented. In China, patients with COVID-19 were immediately isolated in designated existing hospitals, and new hospitals were rapidly built to manage the increasing numbers of cases in the most affected areas
