Optimization of SARS-CoV-2 laboratory testing in a rural healthcare facility in the United States

Authors

  • Tanvi S. Bharathan Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA
  • Austan J. Trale Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA
  • Tashi Bharathan Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA
  • Nichol L. Dienes Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA
  • Jackie Sansig Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA
  • Steven Wilson Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA
  • Narayanaswamy Bharathan Indiana University of Pennsylvania, Indiana, Pennsylvania 15701, USA http://orcid.org/0000-0002-8027-7426

DOI:

https://doi.org/10.18203/2394-6040.ijcmph20211732

Keywords:

COVID19, Community medicine, RT-PCR, Rural health

Abstract

Background: The diagnostic testing for SARS-COV-2 (COVID-19) presented a profound challenge to the entire world, dominating the concern of most governments and public health systems, particularly rural community hospitals in the United States. Indiana University of Pennsylvania (IUP) in partnership with Indiana Regional Medical Center (IRMC) began on site, same-day COVID-19 testing in efforts to not only combat the challenges that health providers faced in rural Indiana community but also help to strengthen global diagnostic capacity.

Methods: Clinical samples were collected as dry swabs from the nasopharyngeal (NP) regions and processed in phosphate buffer saline (PBS). The crude RNA was directly tested using real-time (RT) reverse transcription quantitative polymerase chain reaction (RT-qPCR) with PrimeDirect probe RT-qPCR Mix (Takara Bio USA) and optimized with probe-primer sets [Integrated DNA Technologies (IDT)].

Results: Validation experiments with dry swabs from NP clinical samples showed no difference in the testing accuracy to those collected in viral transport medium or universal transport medium. Extraction of COVID-19 RNA in PBS reduced processing time of a batch of 50 NP clinical samples from 6 hours to an hour. This allowed for rapid diagnostic testing of nearly 200 clinical samples per day. Optimization of analytical variables helped to detect virus loads up to 2.0 copies/μl during routine diagnostic testing.

Conclusions: During an infectious outbreak, the ideal response by public health authorities is rapid testing. The collaboration between IUP and IRMC attests to the importance of teamwork between local initiatives to detect and prevent further spread within a rural community.

Author Biographies

Tanvi S. Bharathan, Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA

MBBS, MS Public Health Service, Technical Assistant

Austan J. Trale, Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA

BS Pre-Medicine, Technical assistant

Tashi Bharathan, Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA

BS Pre-Medicine, Technical assistant

Nichol L. Dienes, Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA

MLS (ASCP)

Clinical Lab Scientist

Jackie Sansig, Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA

MHA, MT (ASCP)

Administrative Director of Laboratory Medicine,

Toxicology Laboratory

and Respiratory Services

Steven Wilson, Indiana Regional Medical Center, 835 hospital Road, Indiana, Pennsylvania 15701, USA

MD (Doctor of Medicine) Comprehensive Breast Cancer

Narayanaswamy Bharathan, Indiana University of Pennsylvania, Indiana, Pennsylvania 15701, USA

Professor and Chair Biology Department

References

World Health Organization Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases. 2020, March 7. Available at: https://www.who.int/publications-detail/laboratory-testing-for-2019-novel-coronavirus-in-suspected-human-cases-20200117. Accessed on 9 February 2021.

Centers for Disease Control Interim guidelines for collecting, handling, and testing clinical specimens from persons for coronavirus disease 2019 (COVID19) 2020. Available at: https://www.cdc.gov/coronavirus/2019nCoV/lab/guidelines-clinical-specimens.html. Accessed on 09 February 2021.

LabCorp launches test for coronavirus disease 2019 (COVID-19). Laboratory Corporation of America, News release. March 5, 2020. Available at: ir.labcorp.com/newsreleases/newsreleasedetails/labcorp-launches-test-coronavirus-disease-2019-covid-19. Accessed on: 09 February 2021.

Hinton, D. M. Emergency use authorization for the 2019-nCoV Real-Time RT-PCR Diagnostic Panel (Centers for Disease Control and Prevention). US: Food & Drug Administration, March 15, 2020:1–12.

TaqPath COVID-19 Multiplex Diagnostic Solution. ThermoFisherScientific. Available at:www.thermofisher.com/us/en/home/clinical/clinical-genomics/pathogen-detection solutions/coronavirus-2019-ncov/genetic analysis/taqpath-rt-pcr-covid-19-kit.html, Accessed on 29 April 2020.

Chen X, Zhou B, Li M, Liang X, Wang H, Yang G, et al. Serology of severe acute respiratory syndrome: implications for surveillance and outcome. J Infect Dis. 2004;189(7):1158-63.

Chan CM, Tse H, Wong SS, Woo PC, Lau SK, Chen L, Zheng BJ, et al. Examination of seroprevalence of coronavirus HKU1 infection with S protein-based ELISA and neutralization assay against viral spike pseudotyped virus. J Clin Virol. 2009;45(1):54-60.

Tang YW, Schmitz JE, Persing DH, Stratton CW. Laboratory Diagnosis of COVID-19: Current Issues and Challenges. J Clin Microbiol. 2020;58(6):00512-20.

Serology Based tests for COVID-19. John Hopkin Center for Health Surety Available at: https://www.centerforhealthsurity.org/resources/COVID-19/serology/Serology-based-tests-for-COVID-19.html. Accessed on 9 February 2021.

Loeffelholz MJ, Tang YW. Laboratory diagnosis of emerging human coronavirus infections - the state of the art. Emerg Microbes Infect. 2020;9(1):747-56.

Chen Y, Chan KH, Hong C, Kang Y, Ge S, Chen H, et al. A highly specific rapid antigen detection assay for on-site diagnosis of MERS. J Infect. 2016;73(1):82-4.

Lau SK, Woo PC, Wong BH, Tsoi HW, Woo GK, Poon RW, et al. Detection of severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein in sars patients by enzyme-linked immunosorbent assay. J Clin Microbiol. 2004;42(7):2884-9.

Chu DKW, Pan Y, Cheng SMS, Hui KPY, Krishnan P, Liu Y, Ng DYM, Wan CKC, Yang P, Wang Q, Peiris M, Poon LLM. Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia. Clin Chem. 2020;66(4):549-55.

Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25(3):2000045.

Lan L, Xu D, Ye G, Xia C, Wang S, Li Y et al. Positive RT-PCR Test Results in Patients Recovered from COVID-19. Jama. 2020;7.

Li L, Shim T, Zapanta PE. Optimization of COVID-19 testing accuracy with nasal anatomy education. Am J Otolaryngol. 2021 Jan-Feb;42(1):102777.

Wang W, Xu Y, Gao R, Lu R, Han K, Wu G, Tan W. Detection of SARS-CoV-2 in Different Types of Clinical Specimens. JAMA. 2020;323(18):1843-4.

Zou L, Ruan F, Huang M, Liang L, Huang H, Hong Z, Yu J, et al. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients. N Engl J Med. 2020;382(12):1177-9.

Yang Y, Yang M, Shen C, et al. Laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections. The innovation. 2020;3(1):100061.

Holshue ML, DeBolt C, Lindquist S, Lofy KH, Wiesman J, Bruce H,et al; Washington State 2019-nCoV Case Investigation Team. First Case of 2019 Novel Coronavirus in the United States. N Engl J Med. 2020;382(10):929-36.

Lippi G, Simundic AM, Plebani M. Potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19). Clin Chem Lab Med. 2020;58(7):1070-6.

Li J., Ye G, Chen L, Wang J, Li Y. Analysis and countermeasures of false negative results of new coronavirus (2019-nCoV) nucleic acid test. Chinese J Lab Med. 2020:43.

Pan Y, Long L, Zhang D, Yuan T, Cui S, Yang P, Wang Q, Ren S. Potential False-Negative Nucleic Acid Testing Results for Severe Acute Respiratory Syndrome Coronavirus 2 from Thermal Inactivation of Samples with Low Viral Loads. Clin Chem. 2020;66(6):794-801.

Won J, Lee S, Park M, Kim TY, Park MG, Choi BY, et al. Development of a Laboratory-safe and Low-cost Detection Protocol for SARS-CoV-2 of the Coronavirus Disease 2019 (COVID-19). Exp Neurobiol. 2020;29(2):107-19.

Park M, Won J, Choi BY, Lee CJ. Optimization of primer sets and detection protocols for SARS-CoV-2 of coronavirus disease 2019 (COVID-19) using PCR and real-time PCR. Exp Mol Med. 2020;52(6):963-77.

Pan Y, Zhang D, Yang P, Poon LLM, Wang Q. Viral load of SARS-CoV-2 in clinical samples. Lancet Infect Dis. 2020;20(4):411-2.

Yu F, Yan L, Wang N, Yang S, Wang L, Tang Y, et al. Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients. Clin Infect Dis. 2020 ;71(15):793-8.

Peters DJ. Community Susceptibility and Resiliency to COVID-19 Across the Rural-Urban Continuum in the United States. J Rural Health. 2020;36(3):446-56.

NPR. Small‐town hospitals are closing just as coronavirus arrives in rural America. 2020; Available at: https://www.npr.org/2020/04/09/829753752/small-town-hospitals-are-closing-just-as-coronavirus-arrives-in-rural-america. Accessed on 9 February 2021.

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Published

2021-04-27

How to Cite

Bharathan, T. S., Trale, A. J., Bharathan, T., Dienes, N. L., Sansig, J., Wilson, S., & Bharathan, N. (2021). Optimization of SARS-CoV-2 laboratory testing in a rural healthcare facility in the United States. International Journal Of Community Medicine And Public Health, 8(5), 2155–2164. https://doi.org/10.18203/2394-6040.ijcmph20211732

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Section

Original Research Articles