#Facility-Wide #Testing for #SARS-CoV-2 in Nursing Homes — Seven #US Jurisdictions, March–June 2020 (MMWR Morb Mortal Wkly Rep., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), MMWR Morbidity and Mortality Weekly Report, full page: (LINK). Abstract, edited.]

Facility-Wide Testing for SARS-CoV-2 in Nursing Homes — Seven U.S. Jurisdictions, March–June 2020

Early Release / August 11, 2020 / 69

Kelly M. Hatfield, MSPH1; Sujan C. Reddy, MD1; Kaitlin Forsberg, MPH1; Lauren Korhonen, MSPH1; Kelley Garner, MPH2; Trent Gulley, MPH2; Allison James, DVM, PhD2; Naveen Patil, MD2; Carla Bezold, ScD3; Najibah Rehman, MD3; Marla Sievers, MPH4; Benjamin Schram, MPH5; Tracy K. Miller, PhD5; Molly Howell, MPH5; Claire Youngblood, MA6; Hannah Ruegner, MPH6; Rachel Radcliffe, DVM6; Allyn Nakashima, MD7; Michael Torre, PhD7; Kayla Donohue, MPH8; Paul Meddaugh, MS8; Mallory Staskus, MS8; Brandon Attell, MA1; Caitlin Biedron, MD1; Peter Boersma, MPH1; Lauren Epstein, MD1; Denise Hughes1; Meghan Lyman, MD1; Leigh E. Preston, DrPH1; Guillermo V. Sanchez, MSHS, MPH1; Sukarma Tanwar, MMed1; Nicola D. Thompson, PhD1; Snigdha Vallabhaneni, MD1; Amber Vasquez, MD1; John A. Jernigan, MD1

Corresponding author: Kelly M. Hatfield, khatfield2@cdc.gov.

1CDC COVID-19 Response Team; 2Arkansas Department of Health; 3Detroit Health Department, Detroit, Michigan; 4New Mexico Department of Health; 5North Dakota Department of Health; 6South Carolina Department of Health and Environmental Control; 7Utah Department of Health; 8Vermont Department of Health.

All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. Kayla Donohue reports full-time employment at United Way of Northwest Vermont with temporary assignment to COVID-19 response at the Vermont Department of Health, which supported her work related to this publication. No other potential conflicts of interest were disclosed.

Suggested citation for this article: Hatfield KM, Reddy SC, Forsberg K, et al. Facility-Wide Testing for SARS-CoV-2 in Nursing Homes — Seven U.S. Jurisdictions, March–June 2020. MMWR Morb Mortal Wkly Rep. ePub: 11 August 2020. DOI: http://dx.doi.org/10.15585/mmwr.mm6932e5

 

Summary

  • What is already known about this topic?
    • Facility-wide testing of health care personnel and nursing home residents for SARS-CoV-2 can inform strategies to prevent transmission.
  • What is added by this report?
    • In two health department jurisdictions, testing in facilities without a previous COVID-19 case identified a prevalence of 0.4%. Five health department jurisdictions that targeted facility-wide testing after identification of a case found a prevalence of 12%; for each additional day before completion of initial facility-wide testing, an estimated 1.3 additional cases were identified.
  • What are the implications for public health practice?
    • Performing facility-wide testing rapidly following identification of a case in a nursing home might facilitate control of transmission among residents and health care personnel. Strategies are needed to optimize facility-wide testing in nursing homes without a reported case.

 

Abstract

Undetected infection with SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19) contributes to transmission in nursing homes, settings where large outbreaks with high resident mortality have occurred (1,2). Facility-wide testing of residents and health care personnel (HCP) can identify asymptomatic and presymptomatic infections and facilitate infection prevention and control interventions (3–5). Seven state or local health departments conducted initial facility-wide testing of residents and staff members in 288 nursing homes during March 24–June 14, 2020. Two of the seven health departments conducted testing in 195 nursing homes as part of facility-wide testing all nursing homes in their state, which were in low-incidence areas (i.e., the median preceding 14-day cumulative incidence in the surrounding county for each jurisdiction was 19 and 38 cases per 100,000 persons); 125 of the 195 nursing homes had not reported any COVID-19 cases before the testing. Ninety-five of 22,977 (0.4%) persons tested in 29 (23%) of these 125 facilities had positive SARS-CoV-2 test results. The other five health departments targeted facility-wide testing to 93 nursing homes, where 13,443 persons were tested, and 1,619 (12%) had positive SARS-CoV-2 test results. In regression analyses among 88 of these nursing homes with a documented case before facility-wide testing occurred, each additional day between identification of the first case and completion of facility-wide testing was associated with identification of 1.3 additional cases. Among 62 facilities that could differentiate results by resident and HCP status, an estimated 1.3 HCP cases were identified for every three resident cases. Performing facility-wide testing immediately after identification of a case commonly identifies additional unrecognized cases and, therefore, might maximize the benefits of infection prevention and control interventions. In contrast, facility-wide testing in low-incidence areas without a case has a lower proportion of test positivity; strategies are needed to further optimize testing in these settings.

(…)

Keywords: SARS-CoV-2; COVID-19; Diagnostic tests; Institutional outbreaks; USA.

——

#Molecular and #Immunological Diagnostic #Tests of #COVID19: Current Status and Challenges (iScience, abstract)

[Source: iScience, full page: (LINK). Abstract, edited.]

Molecular and Immunological Diagnostic Tests of COVID-19: Current Status and Challenges

Tugba Kilic, Ralph Weissleder, Hakho Lee

Open Access | Published: July 25, 2020 | DOI: https://doi.org/10.1016/j.isci.2020.101406

 

Summary

Rapid spread of coronavirus disease 2019 (COVID-19) is ravaging the globe. Since its first report in December 2019, COVID-19 cases have exploded to over 14 million as of July 2020, claiming more than 600,000 lives. Implementing fast and widespread diagnostic tests is paramount to contain COVID-19, given the current lack of an effective therapeutic or vaccine. This review focuses on a broad description of currently available diagnostic tests to detect either the virus (SARS-CoV-2) or virus-induced immune responses. We specifically explain the working mechanisms of these tests and compare their analytical performance. These analyses will assist in selecting most effective tests for a given application, for example, epidemiology or global pandemic research, population screening, hospital-based testing, home-based and point-of-care testing, and therapeutic trials. Finally, we lay out the shortcomings of certain tests and future needs.

Keywords: SARS-CoV-2; COVID-19; Diagnostic tests.

——

#SARS-CoV-2-specific #antibody #detection for #seroepidemiology: a multiplex analysis approach accounting for accurate #seroprevalence (J Infect Dis., abstract)

[Source: Journal of Infectious Diseases, full page: (LINK). Abstract, edited.]

SARS-CoV-2-specific antibody detection for sero-epidemiology: a multiplex analysis approach accounting for accurate seroprevalence

Gerco den Hartog, Rutger M Schepp, Marjan Kuijer, Corine GeurtsvanKessel, Josine van Beek, Nynke Rots, Marion P G Koopmans, Fiona R M van der Klis, Robert S van Binnendijk

The Journal of Infectious Diseases, jiaa479, https://doi.org/10.1093/infdis/jiaa479

Published: 08 August 2020

 

ABSTRACT

Background

The COVID-19 pandemic necessitates a better understanding of the kinetics of antibody production induced by infection with SARS-CoV-2. We aimed to develop a high throughput multiplex assay to detect antibodies to SARS-CoV-2 to assess immunity to the virus in the general population.

Methods

Spike protein subunits S1 and RBD, and Nucleoprotein were coupled to distinct microspheres. Sera collected before the emergence of SARS-CoV-2 (N=224), and of non-SARS-CoV-2 influenza-like illness (N=184), and laboratory-confirmed cases of SARS-CoV-2 infection (N=115) with various severity of COVID-19 were tested for SARS-CoV-2-specific concentrations of IgG.

Results

Our assay discriminated SARS-CoV-2-induced antibodies and those induced by other viruses. The assay obtained a specificity between 95.1 and 99.0% with a sensitivity ranging from 83.6-95.7%. By merging the test results for all 3 antigens a specificity of 100% was achieved with a sensitivity of at least 90%. Hospitalized COVID-19 patients developed higher IgG concentrations and the rate of IgG production increased faster compared to non-hospitalized cases.

Conclusions

The bead-based serological assay for quantitation of SARS-CoV-2-specific antibodies proved to be robust and can be conducted in many laboratories. Finally, we demonstrated that testing of antibodies against different antigens increases sensitivity and specificity compared to single antigen-specific IgG determination.

COVID-19, IgG, Spike S1, RBD, Nucleoprotein, endemic coronavirus, multiplex bead-based immune assay, specificity, sensitivity, Influenza-like Illness (ILI)

Topic:  epidemiology – coronavirus – antibody formation – antigens – immunity – laboratory – microspheres – nucleoproteins – protein subunits – serologic tests – immunoglobulin g – infections – antibodies – kinetics – viruses – severe acute respiratory syndrome – serum – flu-like illness – laboratory test finding – seroprevalence – sars-cov-2 –
covid-19 – coronavirus pandemic

Issue Section: Major Article

This content is only available as a PDF.

© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Keywords: SARS-CoV-2; COVID-19; Serology; Seroprevalence.

——

#Clinical #Course and #Molecular #Viral #Shedding Among #Asymptomatic and Symptomatic Patients With #SARS-CoV-2 Infection in a #Community #Treatment Center in the Republic of #Korea (JAMA Intern Med., abstract)

[Source: JAMA Internal Medicine, full page: (LINK). Abstract, edited.]

Clinical Course and Molecular Viral Shedding Among Asymptomatic and Symptomatic Patients With SARS-CoV-2 Infection in a Community Treatment Center in the Republic of Korea

Seungjae Lee, MD1; Tark Kim, MD2; Eunjung Lee, MD1; Cheolgu Lee, MD3; Hojung Kim, MD4; Heejeong Rhee, MD5; Se Yoon Park, MD1; Hyo-Ju Son, MD1; Shinae Yu, MD6; Jung Wan Park, MD6; Eun Ju Choo, MD2; Suyeon Park, MS7; Mark Loeb, MD8; Tae Hyong Kim, MD1

Author Affiliations: 1 Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Republic of Korea; 2 Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Republic of Korea; 3 Department of Surgery, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Republic of Korea; 4 Department of Emergency Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Republic of Korea; 5 Department of Family Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Republic of Korea; 6 Department of Internal Medicine, Soonchunhyang University Cheonan Hospital, Soonchunhyang University College of Medicine, Cheonan, Republic of Korea; 7 Department of Biostatistics, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea; 8 Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada

JAMA Intern Med. Published online August 6, 2020.  doi:10.1001/jamainternmed.2020.3862

 

Key Points

  • Question  – Are there viral load differences between asymptomatic and symptomatic patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection?
  • Findings  – In this cohort study that included 303 patients with SARS-CoV-2 infection isolated in a community treatment center in the Republic of Korea, 110 (36.3%) were asymptomatic at the time of isolation and 21 of these (19.1%) developed symptoms during isolation. The cycle threshold values of reverse transcription–polymerase chain reaction for SARS-CoV-2 in asymptomatic patients were similar to those in symptomatic patients.
  • Meaning  – Many individuals with SARS-CoV-2 infection remained asymptomatic for a prolonged period, and viral load was similar to that in symptomatic patients; therefore, isolation of infected persons should be performed regardless of symptoms.

 

Abstract

Importance  

There is limited information about the clinical course and viral load in asymptomatic patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Objective  

To quantitatively describe SARS-CoV-2 molecular viral shedding in asymptomatic and symptomatic patients.

Design, Setting, and Participants  

A retrospective evaluation was conducted for a cohort of 303 symptomatic and asymptomatic patients with SARS-CoV-2 infection between March 6 and March 26, 2020. Participants were isolated in a community treatment center in Cheonan, Republic of Korea.

Main Outcomes and Measures  

Epidemiologic, demographic, and laboratory data were collected and analyzed. Attending health care personnel carefully identified patients’ symptoms during isolation. The decision to release an individual from isolation was based on the results of reverse transcription–polymerase chain reaction (RT-PCR) assay from upper respiratory tract specimens (nasopharynx and oropharynx swab) and lower respiratory tract specimens (sputum) for SARS-CoV-2. This testing was performed on days 8, 9, 15, and 16 of isolation. On days 10, 17, 18, and 19, RT-PCR assays from the upper or lower respiratory tract were performed at physician discretion. Cycle threshold (Ct) values in RT-PCR for SARS-CoV-2 detection were determined in both asymptomatic and symptomatic patients.

Results  

Of the 303 patients with SARS-CoV-2 infection, the median (interquartile range) age was 25 (22-36) years, and 201 (66.3%) were women. Only 12 (3.9%) patients had comorbidities (10 had hypertension, 1 had cancer, and 1 had asthma). Among the 303 patients with SARS-CoV-2 infection, 193 (63.7%) were symptomatic at the time of isolation. Of the 110 (36.3%) asymptomatic patients, 21 (19.1%) developed symptoms during isolation. The median (interquartile range) interval of time from detection of SARS-CoV-2 to symptom onset in presymptomatic patients was 15 (13-20) days. The proportions of participants with a negative conversion at day 14 and day 21 from diagnosis were 33.7% and 75.2%, respectively, in asymptomatic patients and 29.6% and 69.9%, respectively, in symptomatic patients (including presymptomatic patients). The median (SE) time from diagnosis to the first negative conversion was 17 (1.07) days for asymptomatic patients and 19.5 (0.63) days for symptomatic (including presymptomatic) patients (P = .07). The Ct values for the envelope (env) gene from lower respiratory tract specimens showed that viral loads in asymptomatic patients from diagnosis to discharge tended to decrease more slowly in the time interaction trend than those in symptomatic (including presymptomatic) patients (β = −0.065 [SE, 0.023]; P = .005).

Conclusions and Relevance  

In this cohort study of symptomatic and asymptomatic patients with SARS-CoV-2 infection who were isolated in a community treatment center in Cheonan, Republic of Korea, the Ct values in asymptomatic patients were similar to those in symptomatic patients. Isolation of asymptomatic patients may be necessary to control the spread of SARS-CoV-2.

Keywords: SARS-CoV-2; COVID-19; Diagnostic tests; S. Korea.

——

Using #Virus #Sequencing to Determine #Source of #SARS-CoV-2 #Transmission for #HCW (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 26, Number 10—October 2020 | Research Letter

Using Virus Sequencing to Determine Source of SARS-CoV-2 Transmission for Healthcare Worker

Nasia Safdar  , Gage K. Moreno, Katarina M. Braun, Thomas C. Friedrich, and David H. O’Connor

Author affiliations: University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA (N. Safdar); William S. Middleton Memorial Veterans Hospital, Madison (N. Safdar); University of Wisconsin–Madison, Madison (G.K. Moreno, K.M. Braun, T.C. Friedrich, D.H. O’Connor)

 

Abstract

Whether a healthcare worker’s severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is community or hospital acquired affects prevention practices. We used virus sequencing to determine that infection of a healthcare worker who cared for 2 SARS-CoV-2–infected patients was probably community acquired. Appropriate personal protective equipment may have protected against hospital-acquired infection.

Keywords: SARS-CoV-2; COVID-19; HCWs; Diagnostic tests.

——

#Clinical #Predictors and #Timing of Cessation of #Viral #RNA #Shedding in Patients with #COVID19 (J Clin Virol., abstract)

[Source: Journal of Clinical Virology, full page: (LINK). Abstract, edited.]

Journal of Clinical Virology | Available online 5 August 2020, 104577 | In Press, Journal Pre-proof

Clinical Predictors and Timing of Cessation of Viral RNA Shedding in Patients with COVID-19

Cristina Corsini Campioli a, Edison Cano Cevallos a,b, Mariam Assi a,1, Robin Patela b,c, Matthew J. Binnicker b,c, John C. O’Horoa d

a Division of Infectious Diseases, Rochester, MN, USA; b Infectious Diseases Research Laboratory, Rochester, MN, USA; c Division of Clinical Microbiology, Rochester, MN, USA; d Division of Pulmonary and Critical Care, Mayo Clinic, Rochester, MN, USA

Received 21 July 2020, Revised 30 July 2020, Accepted 3 August 2020, Available online 5 August 2020.

DOI: https://doi.org/10.1016/j.jcv.2020.104577

 

Highlights

  • Molecular detection of Severe Acute Respiratory Syndrome Coronavirus 2 is critical in the diagnosis of coronavirus disease 2019.
  • The persistence of SARS-CoV-2 RNA shedding in the context of clinical features and comorbidities is understudied.
  • The cumulative cessation of viral shedding rate at 3 weeks from symptom-onset is 44% in our entire cohort.
  • Repeating a SARS-CoV-2 PCR test within 21 days of a laboratory-confirmed COVID-19 diagnosis is considered unnecessary.

 

Abstract

Background

Molecular detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is key in the diagnosis of coronavirus disease 2019 (COVID-19) and has been widely used for followup of cases as a proxy for contagiousness. The persistence of SARS-CoV-2 RNA shedding in the context of clinical features and comorbidities is understudied.

Methods

We retrospectively reviewed laboratory-confirmed COVID-19 adult symptomatic cases at Mayo Clinic, eventually achieving cessation of viral RNA shedding (CVS), defined as two consecutive negative SARS-CoV-2 PCR results on nasopharyngeal swabs collected at least 24 hours apart.

Results

A total of 251 patients were included, median age was 53 years and 59% female. The most common symptoms at diagnosis were cough, myalgia, dyspnea, fever and chills. Myalgia, cough, anosmia, ageusia and sore throat were common at CVS, but fever and dyspnea were not observed. The median time from symptom onset to CVS was 23 days, and did not differ by symptoms. The weekly cumulative CVS rate was 2, 14, 44, 73, 91 and 95% at 1-6 weeks from symptom onset, respectively. Cough and fever were associated with a positive PCR test if tested within 2 weeks of symptoms (P < 0.05). Patients with asthma or immunosuppression were less likely to achieve CVS if tested 3 weeks into symptoms (P < 0.04).

Conclusions

The cumulative CVS rate at 3 weeks from symptom-onset is 44% in our entire cohort. The findings of our study highlight the low yield of repeating a SARS-CoV-2 NP PCR test within 21 days of a laboratoryconfirmed COVID-19 diagnosis.

Keywords: SARS-CoV-2; COVID-19; Diagnostic tests.

——

Unexpected #diagnosis of #COVID19-associated disorders by #SARS-CoV-2-specific #serology (J Clin Virol., abstract)

[Source: Journal of Clinical Virology, full page: (LINK). Abstract, edited.]

Journal of Clinical Virology | Available online 4 August 2020, 104568 | In Press, Journal Pre-proof

Unexpected diagnosis of COVID-19-associated disorders by SARS-CoV-2-specific serology

Hélène Péré a,b,c, Benoit Védie d, Raphaël Vernet e, Nathalie Demory f, Najiby Kassis g, Tristan Mirault b,h, Hélène Lazareth i, Geoffroy Volle j, Elsa Denoix j, David Lebeaux c,k, Isabelle Podglajen c,l, Laurent Bélec a,b,c, David Veyer a,m

a Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France; b INSERM U970, PARCC, Hôpital Européen Georges Pompidou, Faculté de Médecine, Université de Paris, Paris, France; c Faculté de Médecine, Université de Paris, Paris, France; d Laboratoire de Biochimie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France; e Département d’Informatique Médicale, Biostatistiques et Santé Publique, Hôpital Européen Georges Pompidou, Assistance Publique–Hôpitaux de Paris, Paris, France; f Service de Médecine du Travail, Hôpital Européen Georges Pompidou, Assistance Publique–Hôpitaux de Paris, Paris, France; g Unité d’Hygiène Hospitalière, Service de Microbiologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France; h Départment de Médecine Vasculaire, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France; i Service de Néphrologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France; j Département de Médecine Interne, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France; k Unité Mobile d’Infectiologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France; l Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France; m Unité de Génomique Fonctionnelle des Tumeurs Solides, Centre de Recherche des Cordeliers, INSERM, Université Paris, Paris, France

Received 7 July 2020, Accepted 29 July 2020, Available online 4 August 2020.

DOI: https://doi.org/10.1016/j.jcv.2020.104568

 

Abstract

Facing the ongoing pandemic caused by SARS-CoV-2, there is an urgent need for serological assays identifying individuals with on-going infection as well as past coronavirus infectious disease 2019 (COVID-19). We herein evaluated the analytical performances of the CE IVD-labeled Abbott SARS-CoV-2 IgG assay (Des Plaines, IL, USA) carried out with the automated Abbott Architect™ i2000 platform at Hôpital Européen Georges Pompidou, Paris, France, using serum sample panels obtained from health-workers with COVID-19 history confirmed by positive nucleic acid amplification-based diagnosis and from patients randomly selected for whom serum samples were collected before the COVID-19 epidemic. The Abbott SARS-CoV-2 IgG assay showed sensitivity of 94% and specificity of 100%, demonstrating high analytical performances allowing convenient management of suspected on-going and past-infections. In addition, the SARS-CoV-2 IgG positivity rates were compared in COVID-19 positive and COVID-19 free areas from our hospital. Thus, the frequency of SARS-CoV-2-specific IgG was around 10-fold higher in COVID-19 areas than COVID-19 free areas (75% versus 8%; P < 0.001). Interestingly, several inpatients hospitalized in COVID-19 free areas suffering from a wide range of unexplained clinical features including cardiac, vascular, renal, metabolic and infectious disorders, were unexpectedly found seropositive for SARS-CoV-2 IgG by systematic routine serology, suggesting possible causal involvement of SARS-CoV-2 infection. Taken together, these observations highlight the potential interest of SARS-CoV-2-specific serology in the context of COVID-19 epidemic, especially to assess past SARS-CoV-2 infection as well as possible unexpected COVID-19-associated disorders.

Keywords: SARS-CoV-2; COVID-19; Serology; Diagnostic tests.

——

Discrimination of #False #Negative Results in RT – #PCR #Detection of #SARS-CoV-2 #RNAs in Clinical #Specimens by Using an Internal Reference (Virol Sin., abstract)

[Source: Virologica Sinica, full page: (LINK). Abstract, edited.]

Discrimination of False Negative Results in RT-PCR Detection of SARS-CoV-2 RNAs in Clinical Specimens by Using an Internal Reference

Yafei Zhang, Changtai Wang, Mingfeng Han, Jun Ye, Yong Gao, Zhongping Liu, Tengfei He, Tuantuan Li, Mengyuan Xu, Luping Zhou, Guizhou Zou, Mengji Lu & Zhenhua Zhang

Virologica Sinica (2020)

 

Abstract

Reverse transcription-polymerase chain reaction (RT-PCR) is an essential method for specific diagnosis of SARS-CoV-2 infection. Unfortunately, false negative test results are often reported. In this study, we attempted to determine the principal causes leading to false negative results of RT-PCR detection of SARS-CoV-2 RNAs in respiratory tract specimens. Multiple sputum and throat swab specimens from 161 confirmed COVID-19 patients were tested with a commercial fluorescent RT-PCR kit targeting the ORF1ab and N regions of SARS-CoV-2 genome. The RNA level of a cellular housekeeping gene ribonuclease P/MRP subunit p30 (RPP30) in these specimens was also assessed by RT-PCR. Data for a total of 1052 samples were retrospectively re-analyzed and a strong association between positive results in SARS-CoV-2 RNA tests and high level of RPP30 RNA in respiratory tract specimens was revealed. By using the ROC-AUC analysis, we identified Ct cutoff values for RPP30 RT-PCR which predicted false negative results for SARS-CoV-2 RT-PCR with high sensitivity (95.03%–95.26%) and specificity (83.72%–98.55%) for respective combination of specimen type and amplification reaction. Using these Ct cutoff values, false negative results could be reliably identified. Therefore, the presence of cellular materials, likely infected host cells, are essential for correct SARS-CoV-2 RNA detection by RT-PCR in patient specimens. RPP30 could serve as an indicator for cellular content, or a surrogate indicator for specimen quality. In addition, our results demonstrated that false negativity accounted for a vast majority of contradicting results in SARS-CoV-2 RNA test by RT-PCR.

Keywords: SARS-CoV-2; COVID-19; Diagnostic tests.

——

#SARS-CoV-2 Virus #Culture and Subgenomic #RNA for Respiratory #Specimens from Patients with #Mild #Coronavirus Disease (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK): Abstract, edited.]

Volume 26, Number 11—November 2020 | Dispatch

SARS-CoV-2 Virus Culture and Subgenomic RNA for Respiratory Specimens from Patients with Mild Coronavirus Disease

Ranawaka A.P.M. Perera, Eugene Tso, Owen T.Y. Tsang, Dominic N.C. Tsang, Kitty Fung, Yonna W.Y. Leung, Alex W.H. Chin, Daniel K.W. Chu, Samuel M.S. Cheng, Leo L.M. Poon, Vivien W.M. Chuang, and Malik Peiris

Author affiliations: The University of Hong Kong, Hong Kong, China (R.A.P.M. Perera, Y.W.Y. Leung, A.W.H. Chin, D.K.W. Chu, S.M.S. Cheng, L.L.M. Poon, M. Peiris); United Christian Hospital, Hong Kong (E. Tso, K. Fung); Centre for Health Protection, Hong Kong (D.N.C. Tsang); Hospital Authority of Hong Kong, Hong Kong (V.W. M. Chuang); Princess Margaret Hospital, Hong Kong (O.T.Y. Tsang)

 

Abstract

We investigated 68 respiratory specimens from 35 coronavirus disease patients in Hong Kong, of whom 32 had mild disease. We found that severe acute respiratory syndrome coronavirus 2 and subgenomic RNA were rarely detectable beyond 8 days after onset of illness. However, virus RNA was detectable for many weeks by reverse transcription PCR.

Keywords: SARS-CoV-2; COVID-19; Diagnostic tests.

——

Determining the optimal #strategy for reopening #schools, the impact of #test and trace #interventions, and the #risk of occurrence of a second #COVID19 epidemic wave in the UK: a modelling study (Lancet Child Adolesc Health, abstract)

[Source: Lancet Child and Adolescent Health, full page: (LINK). Abstract, edited.]

Determining the optimal strategy for reopening schools, the impact of test and trace interventions, and the risk of occurrence of a second COVID-19 epidemic wave in the UK: a modelling study

Jasmina Panovska-Griffiths, DPhil, Cliff C Kerr, PhD, Robyn M Stuart, PhD, Dina Mistry, PhD, Daniel J Klein, PhD, Russell M Viner, PhD †, Chris Bonell, PhD †

Published: August 03, 2020 | DOI: https://doi.org/10.1016/S2352-4642(20)30250-9

 

Summary

Background

As lockdown measures to slow the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection begin to ease in the UK, it is important to assess the impact of any changes in policy, including school reopening and broader relaxation of physical distancing measures. We aimed to use an individual-based model to predict the impact of two possible strategies for reopening schools to all students in the UK from September, 2020, in combination with different assumptions about relaxation of physical distancing measures and the scale-up of testing.

Methods

In this modelling study, we used Covasim, a stochastic individual-based model for transmission of SARS-CoV-2, calibrated to the UK epidemic. The model describes individuals’ contact networks stratified into household, school, workplace, and community layers, and uses demographic and epidemiological data from the UK. We simulated six different scenarios, representing the combination of two school reopening strategies (full time and a part-time rota system with 50% of students attending school on alternate weeks) and three testing scenarios (68% contact tracing with no scale-up in testing, 68% contact tracing with sufficient testing to avoid a second COVID-19 wave, and 40% contact tracing with sufficient testing to avoid a second COVID-19 wave). We estimated the number of new infections, cases, and deaths, as well as the effective reproduction number (R) under different strategies. In a sensitivity analysis to account for uncertainties within the stochastic simulation, we also simulated infectiousness of children and young adults aged younger than 20 years at 50% relative to older ages (20 years and older).

Findings

With increased levels of testing (between 59% and 87% of symptomatic people tested at some point during an active SARS-CoV-2 infection, depending on the scenario), and effective contact tracing and isolation, an epidemic rebound might be prevented. Assuming 68% of contacts could be traced, we estimate that 75% of individuals with symptomatic infection would need to be tested and positive cases isolated if schools return full-time in September, or 65% if a part-time rota system were used. If only 40% of contacts could be traced, these figures would increase to 87% and 75%, respectively. However, without these levels of testing and contact tracing, reopening of schools together with gradual relaxing of the lockdown measures are likely to induce a second wave that would peak in December, 2020, if schools open full-time in September, and in February, 2021, if a part-time rota system were adopted. In either case, the second wave would result in R rising above 1 and a resulting second wave of infections 2·0–2·3 times the size of the original COVID-19 wave. When infectiousness of children and young adults was varied from 100% to 50% of that of older ages, we still found that a comprehensive and effective test–trace–isolate strategy would be required to avoid a second COVID-19 wave.

Interpretation

To prevent a second COVID-19 wave, relaxation of physical distancing, including reopening of schools, in the UK must be accompanied by large-scale, population-wide testing of symptomatic individuals and effective tracing of their contacts, followed by isolation of diagnosed individuals.

Funding

None.

Keywords: SARS-CoV-2; COVID-19; School closure; Diagnostic tests; UK.

——