key: cord-0850128-f22zqa3f authors: Assennato, S. M.; Ritchie, A. V.; Nadala, C.; Zhang, H.; Datir, R.; Gupta, R. K.; Curran, M. D.; Lee, H. H.; Goel, N. title: Performance evaluation of the point-of-care SAMBA II SARS-CoV-2 Test for detection of SARS-CoV-2 date: 2020-05-26 journal: nan DOI: 10.1101/2020.05.24.20100990 sha: 13a057a34f4bcacf709bd5421a14d8f59682f0a5 doc_id: 850128 cord_uid: f22zqa3f Background: Nucleic acid amplification for the detection of SARS-CoV-2 RNA in respiratory samples is the standard method for diagnosis. These tests are centralised and therefore turnaround times can be 2-5 days. Point-of-care testing with rapid turnaround times would allow more effective triage in settings where patient management and infection control decisions need to be made rapidly. Methods: Analytical and clinical sensitivity and specificity of the SAMBA II SARS-CoV-2 Test was evaluated on panels and residual clinical samples. The clinical performance was compared to the Public Health England reference tests. Results: The limit of detection of the SAMBA II SARS-CoV-2 Test is 250 cp/mL and is specific for detection of 2 regions of the SARS-CoV-2 genome. The clinical sensitivity was evaluated in 172 clinical samples provided by Public Health England, Cambridge, which showed a sensitivity of 98.9% (95% CI 94.03-99.97%), specificity of 100% (95% CI 95.55-100%), PPV of 100% and NPV of 98.78% (92.02-99.82%) compared to testing by Public Health England (PHE). SAMBA detected 3 positive samples that were initially negative by PHE. Discussion: The data shows that the SAMBA II SARS-CoV-2 Test performs equivalently to the centralised testing methods with a much quicker turnaround time. Point of care testing, such as SAMBA, should enable rapid patient management and effective implementation of infection control measures. The SARS-CoV-2 was first reported in Wuhan, China, in early December 2019 and is 52 the causative agent of coronavirus disease 19 (COVID-19) [1] . It has since spread to 53 over 188 countries/regions around the world [2], causing 317,234 deaths [3] . It was 54 declared a pandemic by the World Health Organisation on the 11th of March 2020 [4] . 55 In Europe, the country with the highest number of deaths is UK, which as of the 17 th 56 of May has had 243,694 lab-confirmed cases and 34,636 deaths in all settings [5] . Although this test has good accuracy, the samples must be transported to centralized 65 testing laboratories and batched for processing, which leads to turnaround times of 66 around 48 hours or more. This means treatment of severely ill patients may be 67 suboptimal when other causative pathogens are in the differential diagnosis and those 68 requiring admission or triage with possible COVID-19 maybe unnecessarily isolated 69 or inappropriately cohorted in a COVID-19 ward. This causes obvious bottlenecks in 70 addition to the sheer number of samples that require processing; at present hospital 71 and regional laboratories are at full capacity and a rapid point of care (POC) testing is 72 The SAMBA II nucleic acid testing system was originally designed for HIV testing in 74 POC and resource-limited settings, with CE-marked products for early infant diagnosis 75 supernatant was harvested after 24 hours and filtered. Fifty (50) (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 26, 2020. Surplus samples obtained from patients known to be symptomatic for COVID-19 and 173 submitted to the Public Health England Cambridge Laboratory for routine testing were 174 retrieved before being discarded. These samples were rendered anonymous and 175 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The SAMBA II SARS-CoV-2 Test primers and probes for Target 1 (Orf 1ab) had 100% 207 match to all but one available SARS-CoV-2 sequence for this region in the NCBI 208 database (n=157). For this one sequence, a single nucleotide mismatch was found 209 that maps to the capture probe with no predicted impact on the assay performance. 210 The primers and probes for Target 2 (N) had 100% identity to all available SARS-CoV-211 2 sequences for this region in the NCBI database (n=157). showed that only one SAMBA probe (N region) had greater than 80% homology (81%) 225 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 26, 2020. (Table 3 ). The three SAMBA positive samples were repeat 248 positive by SAMBA and on retest by PHE they were found to be borderline positive 249 with high CT values for at least one of the target genes on the Colindale or Cambridge 250 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. turnaround, such as SAMBA II, will be essential not only during high rates of infection 273 but also as the country begins to end the lockdown period and localised outbreaks will 274 need to be managed quickly and efficiently. 275 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 26, 2020. Potential limitations of this study include that the virus inactivation study was carried 299 out using a constructed pseudovirus rather than a SARS-CoV-2 or other coronavirus 300 All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 26, 2020. . https://doi.org/10.1101/2020.05.24.20100990 doi: medRxiv preprint due to availability. Also clinical samples were collected in VTM and diluted 1:2 in SCoV 301 buffer rather than collected directly into SCoV buffer, which may affect the sensitivity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 26, 2020. . https://doi.org/10.1101/2020.05.24.20100990 doi: medRxiv preprint COVID-19 Dashboard by the Center for Systems Science and Engineering WHO Director-General's opening remarks at 318 the media briefing on COVID-19 -11 Tests for viral load monitoring at the point-of-care Leukodepletion 363 as a Point-of-Care Method for Monitoring HIV-1 Viral Load in Whole Blood Full 366 length HIV-1 Gag determines protease inhibitor susceptibility within in 367 vitro assays A blueprint for the implementation of a 371 validated approach for the detection of SARS-Cov2 in clinical samples in 372 academic facilities UK Standards for Microbiology 374 Investigations -Evaluations, validations and verifications of diagnostic tests Biomerieux ARGENE® SARS-CoV-2 R Gene® Instructions for Use Three Sample-To-Answer Platforms for the Detection of SARS-CoV-2 Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid 391 Detection of SARS-CoV-2 The Detection of SARS-CoV-2 using the Cepheid Xpert Xpress SARS CoV-2 and Roche cobas SARS-CoV-2 Assays