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      Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages

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          Highlights

          • •

            High demand for diagnostic testing for COVID-19 has depleted commercially available consumables for diagnostic testing.

          • •

            Alternative swabs that are not approved for Nasopharyngeal sampling work well for COVID-19 diagnostics.

          • •

            Alternative fluids that are readily available in hospital settings can function as alternatives to Viral Transport Media.

          • •

            No meaningful difference in viral yield from different swabs and most transport mediums for the collection and detection of SARS-CoV-2, indicating swab and medium alternatives could be used if supplies run out.

          Abstract

          On March 11, 2020, the World Health Organization (WHO) assessed COVID-19, caused by SARS-CoV-2, as a pandemic. As of June 1, 2020, SARS-CoV-2 has had a documented effect of over 6 million cases world-wide, amounting to over 370,000 deaths (World Health Organization, 2020. Novel Coronavirus (COVID-19) Situation. http:// https://covid19.who.int/). Consequently, the high demand for testing has resulted in a depletion of commercially available consumables, including the recommended swabs and viral transport media (VTM) required for nasopharyngeal sampling. Therefore, the potential use of unvalidated alternatives must be explored to address the global shortage of testing supplies. To tackle this issue, we evaluated the utility of different swabs and transport mediums for the molecular detection of SARS-CoV-2. This study compared the performance of six swabs commonly found in primary and tertiary health care settings (PurFlock Ultra, FLOQSwab, Puritan Pur-Wraps cotton tipped applicators, Puritan polyester tipped applicators, MedPro 6” cotton tipped applicators, and HOLOGIC Aptima) for their efficacy in testing for SARS-CoV-2. Separately, the molecular detection of SARS-CoV-2 was completed from different transport mediums (DMEM, PBS, 100 % ethanol, 0.9 % normal saline and VTM), which were kept up to three days at room temperature (RT). The results indicate that there is no meaningful difference in viral yield from different swabs and most transport mediums for the collection and detection of SARS-CoV-2, indicating swab and medium alternatives could be used if supplies run out.

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          Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

          Victor M Corman, Olfert Landt, Marco Kaiser … (2020)
          Background The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. Aim We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. Methods Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. Results The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project. Conclusion The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.
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            Outbreak of pneumonia of unknown etiology in Wuhan, China: The mystery and the miracle

            Hongzhou Lu, Charles W. Stratton, Yi-Wei Tang (2020)
            Since December 2019, a total of 41 cases of pneumonia of unknown etiology have been confirmed in Wuhan city, Hubei Province, China. Wuhan city is a major transportation hub with a population of more than 11 million people. Most of the patients visited a local fish and wild animal market last month. At a national press conference held today, Dr Jianguo Xu, an academician of the Chinese Academy of Engineering, who led a scientific team announced that a new‐type coronavirus, tentatively named by World Health Organization as the 2019‐new coronavirus (2019‐nCoV), had caused this outbreak. 1 The 2019‐nCoV has a different coronavirus‐specific nucleic acid sequence from known human coronavirus species, which are similar to some of the beta coronaviruses identified in bats. 2 , 3 The virus‐specific nucleic acid sequences were detected in lung fluid, blood and throat swab samples in 15 patients and the virus that was isolated showed a typical coronavirus appearance under electron microscopy. Further research will be conducted to better understand the new coronavirus to develop antiviral agents and vaccines. 4 We applauded the excellent job that has been done so far. The infection was first described in December. Within 9 days, a special team consisted of physicians, scientists and epidemiologists who ruled out several extremely contagious pathogens including SARS, which killed hundreds of people more than a decade ago, and MERS. This has surely alleviated environmental concerns as Hong Kong authorities had quickly stepped up the disinfection of trains and airplanes and checks of passengers due to this outbreak. Most of the patients visited the fish and wild animal market last month in Wuhan. This fish and wild animal market also sold live animals such as poultry, bats, marmots, and snakes. All patients received prompt supportive treatment in quarantine. Among them, seven patients were in serious condition and one patient died. All of the 42 patients so far confirmed were from China except one Thailand patient who was a traveler from Wuhan. Eight patients have been cured of the disease and were discharged from the hospital last week. The 2019‐nCoV now have been isolated from multiple patients and appears to be the culprit. But the mystery has not been completely solved yet. Until there is a formal published scientific manuscript, the facts can be argued, particularly regarding causality despite these facts having been officially announced. The data collected so far is not enough to confirm the causal relationship between the new‐type coronavirus and the respiratory disease based on classical Koch's postulates or modified ones as suggested by Fredricks and Relman. 5 The viral‐specific nucleic acids were only discovered in 15 patients, and successful virus culture was extremely limited to only a few patients. There remains considerable work to be done to differentiate between colonization, shedding, and infection. Additional strains of the 2019‐nCoV need to be isolated to study their homologies. It is expected that antigens and monoclonal antibodies will be developed so serology can be used to confirm previous and acute infection status. The episode demonstrates further the need for rapid and accurate detection and identification methods that can be used in the local hospitals and clinics bearing the burden of identifying and treating patients. Recently, the Clinical Laboratory Improvement Amendments (CLIA) of 1988 has waived highly sensitive and specific molecular devices known as CLIA‐waived devices so that these devices are gradually becoming available for point of care testing. Finally, the epidemiological similarity between this outbreak and that of SARS in 2002‐2003 6 is striking. SARS was then traced to animal markets 7 and eventually to palm civets. 8 Later bats were identified as animal reservoirs. 9 Could this novel coronavirus be originated from wild animals? The family Coronaviridae includes two subfamilies. 10 One, the subfamily Coronavirinae, contains a substantial number of pathogens of mammals that individually cause a remarkable variety of diseases, including pneumonia. In humans, coronaviruses are among the spectrum of viruses that cause the common cold as well as more severe respiratory disease—specifically SARS and MERS, which are both zoonoses. The second subfamily, Torovirinae, contains pathogens of both terrestrial and aquatic animals. The genus Torovirus includes the type species, equine torovirus (Berne virus), which was first isolated from a horse with diarrhea, and the Breda virus, which was first isolated from neonatal calves with diarrhea. White bream virus from fish is the type species of the genus Bafinivirus. However, there is no evidence so far that the seafood from the fish and animal market caused 2019‐nCoV‐associated pneumonia. This epidemiologic similarity clearly provides a starting point for the further investigation of this outbreak. In the meantime, this fish and animal market has been closed until the epidemiological work determines the animal host of this novel coronavirus. Only then will the miracle be complete.
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              Viral load of SARS-CoV-2 in clinical samples

              Yang Pan, Daitao Zhang, Peng Yang … (2020)
              An outbreak caused by a novel human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Wuhan in December 2019, 1 and has since spread within China and to other countries. Real-time RT-PCR assays are recommended for diagnosis of SARS-CoV-2 infection. 2 However, viral dynamics in infected patients are still yet to be fully determined. Here, we report our findings from different types of clinical specimens collected from 82 infected individuals. Serial samples (throat swabs, sputum, urine, and stool) from two patients in Beijing were collected daily after their hospitalisation (patient 1, days 3–12 post-onset; patient 2, days 4–15 post-onset). These samples were examined by an N-gene-specific quantitative RT-PCR assay, as described elsewhere. 3 The viral loads in throat swab and sputum samples peaked at around 5–6 days after symptom onset, ranging from around 104 to 107 copies per mL during this time (figure A, B ). This pattern of changes in viral load is distinct from the one observed in patients with SARS, which normally peaked at around 10 days after onset. 4 Sputum samples generally showed higher viral loads than throat swab samples. No viral RNA was detected in urine or stool samples from these two patients. Figure Viral dynamics of SARS-CoV-2 in infected patients Viral load (mean [SD]) from serial throat swab and sputum samples in patient 1 (A) and patient 2 (B). (C) Viral load (median [IQR]) in throat and sputum samples collected from 80 patients at different stages after disease onset. (D) Correlation between viral load in throat swab samples and viral load in sputum samples. We also studied respiratory samples (nasal [n=1] and throat swabs [n=67], and sputum [n=42]) collected from 80 individuals at different stages of infection. The viral loads ranged from 641 copies per mL to 1·34 × 1011 copies per mL, with a median of 7·99 × 104 in throat samples and 7·52 × 105 in sputum samples (figure C). The only nasal swab tested in this study (taken on day 3 post-onset) showed a viral load of 1·69 × 105 copies per mL. Overall, the viral load early after onset was high (>1 × 106 copies per mL). However, a sputum sample collected on day 8 post-onset from a patient who died had a very high viral load (1·34 × 1011 copies per mL). Notably, two individuals, who were under active surveillance because of a history of exposure to SARS-CoV-2-infected patients showed positive results on RT-PCR a day before onset, suggesting that infected individuals can be infectious before them become symptomatic. Among the 30 pairs of throat swab and sputum samples available, viral loads were significantly correlated between the two sample types for days 1–3 (R2=0·50, p=0·022), days 4–7 (R2=0·93, p<0·001), and days 7–14 (R2=0·95, p=0·028). From 17 confirmed cases of SARS-CoV-2 infection with available data (representing days 0–13 after onset), stool samples from nine (53%; days 0–11 after onset) were positive on RT-PCR analysis. Although the viral loads were less than those of respiratory samples (range 550 copies per mL to 1·21 × 105 copies per mL), precautionary measures should be considered when handling faecal samples.
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                Author and article information

                Contributors
                Lauren Garnett
                Journal
                Journal ID (nlm-ta): J Virol Methods
                Journal ID (iso-abbrev): J. Virol. Methods
                Title: Journal of Virological Methods
                Publisher: Published by Elsevier B.V.
                ISSN (Print): 0166-0934
                ISSN (Electronic): 1879-0984
                Publication date PMC-release: 8 August 2020
                Publication date (Electronic): 8 August 2020
                Electronic Location Identifier: 113947
                Affiliations
                [a ]Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Canada
                [b ]Department of Medical Microbiology and Infectious Diseases, Canada
                [c ]Department of Paediatrics and Child Health, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
                Author notes
                [* ]Corresponding author at: Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Canada. jim.strong@ 123456canada.ca
                Article
                Publisher ID: S0166-0934(20)30199-3 Publisher ID: 113947
                DOI: 10.1016/j.jviromet.2020.113947
                PMC ID: 7414358
                PubMed ID: 32781008
                SO-VID: 0c6df389-e651-4643-be4c-0f5f66f97cb3
                Copyright © © 2020 Published by Elsevier B.V.
                License:

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                Date received : 24 June 2020
                Date revision received : 31 July 2020
                Date accepted : 4 August 2020
                Categories
                Subject: Article

                ScienceOpen disciplines: Microbiology & Virology
                Keywords: sars-cov-2,swab,diagnostic testing
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology
                Keywords: sars-cov-2, swab, diagnostic testing

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