Original Research

COVID-19 Cycle Threshold/Cycle Number Testing at a Community Living Center

Fed Pract. 2022 June;39(6):254-260 | 10.12788/fp.0276

Author(s):

Background: COVID-19 imposes a special risk to the nursing home population, including community living centers (CLCs) for veterans. Cycle threshold/cycle number (CT/CN) values obtained by serial reverse transcriptase polymerase chain reaction (RT-PCR) testing could yield valuable information about viral load and potential infectiousness. Serial testing for COVID- 19 with CT/CN correlates in a nursing home population during an outbreak has not yet been reported in the literature.

Methods: A retrospective review of serial RT-PCR testing for COVID-19 during an outbreak at a CLC was performed from March 28 to April 4, 2020, with follow-up of identified patients until November 10, 2020. Testing was performed on the Abbot m2000 or Cepheid platform.

Results: Of 80 patients tested, 25 (31%) were positive for COVID-19. CT/CN values corresponded to the infection course as expected.

Conclusions: Repeat testing for COVID-19 accompanied by CT/ CN values could provide clinical and epidemiologic information about the likely stage of the patients’ disease course, which may aid public health measures and clinical management.

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References

1. Chen T, Wu D, Chen H, et al. Clinical characteristics of 113 deceased patients with coronavirus disease 2019: retrospective study. BMJ. 2020;368:m1091. doi:10.1136/bmj.m1091

2. Tsan L, Davis C, Langberg R, et al. Prevalence of nursing home-associated infections in the Department of Veterans Affairs nursing home care units. Am J Infect Control. 2008;36(3):173-179. doi:10.1016/j.ajic.2007.06.008

3. Zhou F, Yu T, Du R, et al. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. Lancet. 2020;395(10229):1054-1062. doi:10.1016/S0140-6736(20)30566-3

4. Arentz M, Yim E, Klaff L, et al. Characteristics and outcomes of 21 critically ill patients with COVID-19 in Washington State. JAMA. 2020;323(16):1612-1614. doi:10.1001/jama.2020.4326

5. McMichael TM, Currie DW, Clark S, et al. Public Health–Seattle and King County, EvergreenHealth, and CDC COVID-19 Investigation Team. Epidemiology of Covid-19 in a long-term care facility in King County, Washington. N Engl J Med. 2020;382(21):2005-2011. doi:10.1056/NEJMoa2005412

6. Childs A, Zullo AR, Joyce NR, et al. The burden of respiratory infections among older adults in long-term care: a systematic review. BMC Geriatr. 2019;19(1):210. doi:10.1186/s12877-019-1236-6

7. Eriksen HM, Iversen BG, Aavitsland PJ. Prevalence of nosocomial infections and use of antibiotics in long-term care facilities in Norway, 2002 and 2003. Hosp Infect. 2004;57(4):316-320. doi:10.1016/j.jhin.2004.03.028

8. Magleby R, Westblade LF, Trzebucki A, et al. Impact Severe acute respiratory syndrome coronavirus 2 viral load on risk of intubation and mortality among hospitalized patients with coronavirus disease 2019. Clin Infect Dis. 2021;73(11):e4197-e4205. doi:10.1093/cid/ciaa851

9. Buchan B, Hoff J, Gmehlin C, et al. Distribution of SARSCoV- 2 PCR cycle threshold values provide practical insight into overall and target-specific sensitivity among symptomatic patients. Am Clin Pathol. 2020;154:479-485. doi:10.1093/ajcp/aqaa133

10. He X, Lau EHY, Wu P, et al. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat Med. 2020;26(5):672-675. doi:10.1038/s41591-020-0869-5

11. Zou L, Ruan F, Huang M, et al. SARS-CoV-2 Viral load in upper respiratory specimens of infected patients. N Engl J Med. 2020;382(12):1177-1179. doi:10.1056/NEJMc2001737

12. Singanayagam A, Patel M, Charlett A, et al. Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020. Euro Surveill. 2020;25(32):2001483. doi:10.2807/1560-7917.ES.2020.25.32.2001483

13. Salvatore P, Dawson P, Wadhwa A, et al. Epidemiological correlates of PCR cycles threshold values in the detection of SARS-CoV-2. Clin Infect Dis. 2021;72(11):e761-e767. doi:10.1093/cid/ciaa1469

14. Kissler S, Fauver J, Mack C, et al. Viral dynamics of SARS-CoV-2 infection and the predictive value of repeat testing. medRxiv. 2020;10.21.20217042. doi:10.1101/2020.10.21.20217042 1

5. Escobar DJ, Lanzi M, Saberi P, et al. Mitigation of a COVID-19 outbreak in a nursing home through serial testing of residents and staff. Clin Infect Dis. 2021;72(9):e394- e396. doi:10.1093/cid/ciaa1021

16. Eibner C, Krull H, Brown KM, et al. Current and projected characteristics and unique health care needs of the patient population served by the Department of Veterans Affairs. Rand Health Q. 2016;5(4):13.

17. Agha Z, Lofgren RP, VanRuiswyk JV, Layde PM. Are patients at Veterans Affairs medical centers sicker? A comparative analysis of health status and medical resource use. Arch Intern Med. 2000;160(21):3252-3257. doi:10.1001/archinte.160.21.3252

18. Morgan RO, Teal CR, Reddy SG, Ford ME, Ashton CM. Measurement in Veterans Affairs Health Services Research: veterans as a special population. Health Serv Res. 2005;40(5 Pt 2):1573-1583. doi:10.1111/j.1475-6773.2005.00448.x 1

9. Xpert Xpress SARS-CoV-2. Instructions for use. Cepheid. 302-2562, Rev. C April 2020. Accessed January 7, 2021. https://www.fda.gov/media/136314/download

20. Abbott RealTime SARS-CoV-2. Instructions for use Abbott. 09N77-95. July 2020. Accessed January 7, 2021. https:// www.fda.gov/media/136258/download

21. Petersen JM, Dalal S, Jhala D. Successful implementation of SARS-CoV-2 testing in midst of pandemic with emphasis on all phases of testing. J Clin Pathol. 2021;74:273- 278. doi:10.1136/jclinpath-2020-207175

22. United States Census Bureau. Quick Facts: Philadelphia County, Pennsylvania. Accessed April 16, 2020. https://www .census.gov/quickfacts/philadelphiacountypennsylvania

23. Centers for Disease Control and Prevention. United States COVID-19 cases, deaths, and laboratory testing (NAATS) by state, territory, and jurisdiction. Accessed April 26, 2020. https://www.cdc.gov/coronavirus/2019-ncov/cases -updates/cases-in-us.html 2

4. Petersen J, Jhala D. Ethnicity, comorbid medical conditions, and SARS-CoV-2 test cycle thresholds in the veteran population [published online ahead of print, 2021 Jul 28]. J Racial Ethn Health Disparities. 2021;1-8. doi:10.1007/s40615-021-01114-4

25. Infectious Diseases Society of America, Association for Molecular Pathology. IDSA and AMP joint statement on the use of SARS-CoV-2 PCR cycle threshold (Ct) values for clinical decision-making. Accessed August 28, 2021. https://www.idsociety.org/globalassets/idsa/public-health /covid-19/idsa-amp-statement.pdf

26. Wang J, Ng CY, Brook RH. Response to COVID-19 in Taiwan: big data analysis, new technology, and proactive testing. JAMA. 2020;323(14):1341-1342. doi:10.1001/jama.2020.3151

27. Centers for Disease Control and Prevention. Overview of testing for SARS-CoV-2, the virus that causes COVID- 19. Accessed July 28, 2021. https://www.cdc.gov /coronavirus/2019-ncov/hcp/testing-overview.html

28. Zuvekas SH, Taliaferro GS. Pathways to access: health insurance, the health care delivery system, and racial/ethnic disparities, 1996-1999. Health Aff. 2003;22(2):139-153. doi:10.1377/hlthaff.22.2.139

29. Egede LE. Race, ethnicity, culture, and disparities in health care. J Gen Intern Med. 2006;21(6):667-669. doi:10.1111/j.1525-1497.2006.0512.x

30. Institute of Medicine (US) Committee on Understanding and Eliminating Racial and Ethnic Disparities in Health Care. Smedley BD, Stith AY, Nelson AR, eds. Unequal treatment: confronting racial and ethnic disparities in health care. National Academies Press; 2003. doi:10.17226/12875

31. Ranney ML, Griffeth V, Jha AK. Critical supply shortages – the need for ventilators and personal protective equipment during the Covid-19 Pandemic. N Engl J Med. 2020;382(18):e41. doi:10.1056/NEJMp2006141

COVID-19, caused by SARS-CoV-2, is more severe in individuals with underlying illnesses. Because complete social distancing might be more difficult in nursing homes and community living centers (CLCs), public health leaders and clinicians have been concerned about the epidemiology and disease course in nursing homes even before the COVID-19 pandemic.1-7 A report of a COVID-19 outbreak in a nursing home facility in King County, Washington, documented a 33.7% overall fatality rate for residents and 52.4% among the most critically ill. ^4,5 The experience at King County, Washington, shows that proactive steps to identify, monitor, and apply preventive control measures is important for future outbreaks. ⁵

Reverse transcriptase polymerase chain reaction (RT-PCR) testing produces a cycle threshold (CT) or cycle number (CN) that correlates with viral load and infectiousness. ^8-14 CT/CN represents the number of RT-PCR cycles required for the fluorescent signal to cross the detection threshold (exceed background level) and is inversely proportional to the viral load. Effectively, the higher the viral load, the lower the CT/ CN value (Figure 1). Tracking CT/CN values was not documented in the Washington nursing home outbreak. Reports of COVID- 19 testing in CLCs during outbreaks are sparse, and CT/CN values and demographic distribution of these veterans has not been reported. ¹⁵ The CLC veteran population, with known higher vulnerability to infection and chronic diseases, is epidemiologically different from the general nursing home population. ^15-18 To address these literature gaps, we present the first report of COVID- 19 testing with CT/CN value correlations in the high-risk veteran CLC population.

Methods

A retrospective review of all COVID-19 CT/CN testing at the Corporal Michael J. Crescenz Veterans Affairs Medical Center (VAMC) CLC in Philadelphia, Pennsylvania, from March 28, 2020, to April 24, 2020, was performed with a US Department of Veterans Affairs (VA) Veterans Health Information System Architecture VistA/FileMan search. Only veteran residents were included in this review. Data collected included initial and serial test results, CT/CN on positive test results, test dates, testing platform used, demographic information (age, self-reported ethnicity, and sex), and clinical follow-up information. Health records were reviewed retrospectively to identify death, the first day after diagnosis with no documented symptoms, or hospitalization status.

RT-PCR testing was performed with the Abbott RealTime SARS-CoV-2 assay on the Abbott m2000 platform and the Xpert Xpress SARS-CoV-2 assay on the Cepheid Infinity platform. The Xpert Xpress assay gave 2 CT values for the E and N2 targets on positive samples. ¹⁹ For this assay to indicate a positive specimen, amplification by RT-PCR of the N2 target or both the N2 and E target is required. The Xpert Xpress assay results as presumptive positive if only the E target amplified. This assay counts a maximum of 45 cycles. The Abbott RealTime SARS-CoV-2 assay gave 1 CN derived from the RNA-dependent RNA polymerase and N targets on positive samples.20 The Abbott assay on the m2000 counts a maximum of 37 cycles. The CT/CN value is the number of cycles required by RT-PCR for the fluorescence signal to cross a threshold value exceeding background level. ^19,20