Rapid Large-Scale COVID-19 Testing During Shortages

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.

Keywords: COVID-19; RT-PCR; SARS-CoV-2; preventive testing; testing; validation.

Figure 1

Comparative validation of options for sample collection and for RNA extraction. (A) RNA stability on a standard buccal swab vs. on CentoSwab^TM was compared regarding the fraction of samples testing positive (A₁), and the number of RT-PCR cycles required to reach the signal threshold in RT-PCR (Cp value) (A₂). (B) The ability to extract analyzable RNA was compared between a commercially available system and the in-house-developed regarding the GITC-based system in three independent runs (termed A, B, and C). Parameters used for comparison were the fraction of samples testing positive (B₁), and the number of RT-PCR cycles required to reach the signal threshold in RT-PCR (Cp value) (B₂).

Figure 2

Cohort of tested individuals. (A) Stratification of individuals according to gender. (B) Distribution of ages at testing. (C) Stratification of individuals according to the background. (D) Geographical origin of the tested individuals. In the enlargement to the right, the relative size of the circles denotes the number of individuals from the corresponding area. (E) Distribution of intervals between tests upon recurrent testing. (F) Venn-diagram showing how often the indicated four items were associated with each other.

Figure 3

Genomes of the identified Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) species. (A) To scale scheme of the 29,903 bp viral reference genome as a horizontal black line (NC_045512). Variants detected in at least one of the four sequenced specimens are indicated above; presence of the variant in question in a sample (samples as stippled horizontal lines) is indicated by a colored square. (B) Phylogenetic analysis of the four SARS-CoV-2 genomes (colors corresponding to those used in (A); image generated using tools as provided by Nextstrain [19]). 19A, 19B, 20A, 20B, and 20C denote the currently recognized five major clades; arrows indicate where the presently analyzed virus genomes map in the overall phylogenetic tree.