Rapid Large-Scale COVID-19 Testing During Shortages.

Arndt Rolfs,Mandy Radefeldt,Katja Bruesehafer,Volkmar Weckesser,Krishna K Kandaswamy,Christian Beetz,Vivi Lieu,Filipa Curado,Florian Vogel,Claudia Pöppel,Stephan Schäfer,Susann Krake,Volha Skrahina,Hanaa Gaber,Toni M Förster,Peter Bauer,Jefri J Paul

doi:10.3390/diagnostics10070464

Abstract

The Coronavirus disease 2019 (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in economic and social lockdowns in most countries all over the globe. Early identification of infected individuals is regarded as one of the most important prerequisites for fighting the pandemic and for returning to a ‘New Normal’. Large-scale testing is therefore crucial, but is facing several challenges including shortage of sample collection tools and of molecular biological reagents, and the need for safe electronic communication of medical reports. We present the successful establishment of a holistic SARS-CoV-2 testing platform that covers proband registration, sample collection and shipment, sample testing, and report issuing. The RT-PCR-based virus detection, being central to the platform, was extensively validated: sensitivity and specificity were defined as 96.8% and 100%, respectively; intra-run and inter-run precision were <3%. A novel type of sample swab and an in-house-developed RNA extraction system were shown to perform as good as commercially available products. The resulting flexibility guarantees independence from the current bottlenecks in SARS-CoV-2 testing. Based on our technology, we offered testing at local, national, and global levels. In the present study, we report the results from approx. 18,000 SARS-CoV-2 tests in almost 10,000 individuals from a low-frequency SARS-CoV-2 pandemic area in a homogenous geographical region in north-eastern Germany for a period of 10 weeks (21 March to 31 May 2020). Among the probands, five SARS-CoV-2 positive cases were identified. Comparative analysis of corresponding virus genomes revealed a diverse origin from three of the five currently recognized SARS-CoV-2 phylogenetic clades. Our study exemplifies how preventive SARS-CoV-2 testing can be set up in a rapid and flexible manner. The application of our test has enabled a safe maintenance/resume of critical local infrastructure, e.g., nursing homes where more than 5000 elderlies and caretakers got tested. The strategy outlined by the present study may serve as a blueprint for the implementation of large-scale preventive SARS-CoV-2 testing elsewhere.

Highlights

Corona Virus Disease 2019 (COVID-19) is caused by a novel coronavirus named Severe AcuteRespiratory Syndrome Coronavirus 2 (SARS-CoV-2) [1]
Our findings suggest that the reported concept may serve as a blueprint for entering the ‘New Normal’ during times of COVID-19, and for how to effectively fight similar outbreaks in the future
A web application to be used on smartphones, tablets, and personal computers was developed as information technology support for our holistic SARS-CoV-2 testing approach

Summary

Introduction

Corona Virus Disease 2019 (COVID-19) is caused by a novel coronavirus named Severe AcuteRespiratory Syndrome Coronavirus 2 (SARS-CoV-2) [1]. In December 2019, the first infections were reported from Wuhan (China), and COVID-19 was declared a pandemic by the World Health Organization (WHO) on 11 March 2020. With the respiratory tract being the primary body entry site for SARS-CoV-2 [3], bronchoalveolar fluid, as well as nasopharyngeal and oropharyngeal samples, have been suggested for detection of acute infection [4,5]. The latter two are amenable to outpatient sampling, but oropharyngeal sampling is less discomforting and easier to perform, including in a self-sampling setting [6]. Wet pharyngeal sampling (i.e., usage of a transport medium) and dry pharyngeal sampling (no medium involved) are generally considered to perform well [7]

Methods

Results

Conclusion