key: cord-0812174-e80b629j
authors: Karahasan Yagci, Ayşegul; Can Sarinoglu, Rabia; Bilgin, Huseyin; Yanılmaz, Özgür; Sayın, Elvan; Guneser, Deniz; Öncü, Mehmet Mucahit; Kartal, Zahide Doyuk; Can, Barıs; Kuzan, Beyza Nur; Bülent, Aslan; Korten, Volkan; Cimsit, Cagatay
title: Relationship of the Cycle Threshold Values of SARS-CoV-2 Polymerase Chain Reaction and Total Severity Score of Computerized Tomography in Patients with COVID 19
date: 2020-09-28
journal: Int J Infect Dis
DOI: 10.1016/j.ijid.2020.09.1449
sha: ad37506d3e2443ca1ff863c6692dd6fb7871bf7f
doc_id: 812174
cord_uid: e80b629j

Aim There are limited number of studies analyzing viral load in COVID19 patients and any data that compare viral load to chest computerized tomography (CT) severity. This study aims to evaluate the severity of chest CT in reverse transcriptase polymerase chain reaction (RT-PCR) positive patients and factors associated with it. Methodology SARS-CoV-2 RNA was extracted from nasopharyngeal swab samples by using Bio-speedy viral nucleic acid buffer. RT-PCR test was performed with primers and probes targeting the RdRp gene (Bioexen LTD, Turkey) and results were quantified as Cycle threshold (Ct) values. Chest CT of SARS-CoV-2 RNA positive patients (n: 730) in a period between March 22 and May 20, 2020 were evaluated. Total severity score (TSS) of chest CT ranged 0-20 was calculated by summing up degree of acute lung inflammation lesions involvement of each of the five lung lobes. Results Out of the 284 patients that were hospitalized, 27 (9.5%) of them died. In a total of 236 (32.3%) patients, there were no findings in CT and 216 (91.5%) of them were outpatients (median age 35). TSS was significantly higher in hospitalized patients although only 5.3% had severe changes. Ct values were lower among outpatients indicating higher viral load. An inverse relation between viral load and TSS was detected in both groups. CT severity was related with age and older patients had higher TSS (p < 0.01). Conclusion Viral load is not a critical factor for hospitalisation and mortality whereas outpatients have considerable amount of virus in their nasopharynx that makes them contagious to their contacts. Viral load is important to detect early stages of COVID-19 to minimize potential spread, whereas chest CT can help identify cases requiring extensive medical care.

World Health Organization (WHO) declared the outbreak of novel coronavirus disease (COVID-19) as a Public Health Emergency of International concern on Jan 30, 2020. The first case detected on March In asymptomatic individuals who have been in close contact with symptomatic persons, the rate of positivity could reach 50% without any evidence of symptoms or proven infection (4) . There are limited number of studies that give the amount of SARS-CoV-2 RNA in clinical specimens by reporting cycle threshold (Ct) value for RT-PCR. The Ct (cycle threshold) is defined as the number of cycles required for the fluorescent signal to cross the threshold. Ct levels are inversely proportional to the amount of target nucleic acid in the sample (ie the lower the Ct level the greater the amount of target nucleic acid in the sample.

Chest CT, as a routine imaging tool for pneumonia diagnosis, is relatively easy to perform and can produce fast diagnosis of COVID-19. Chest CT demonstrates typical radiographic features in COVID-19 patients, including ground-glass opacities, multifocal patchy consolidation, and/or interstitial changes with a peripheral distribution (5) . With RT-PCR results as reference in 1014 patients, the sensitivity, specificity, accuracy of chest CT in J o u r n a l P r e -p r o o f 4 indicating COVID-19 infection were 97% (580/601), 25% (105/413) and 68% (685/1014), respectively (6) . Although some studies suggest RT-PCR testing has a limited sensitivity and chest CT has a superb sensitivity for COVID-19, these reports used limited methods (7) .

Hereby we evaluated chest CT results of SARS CoV-2 RT-PCR positive patients. The total severity score (TSS) was suggested to quantify pulmonary inflammation and correlate to the clinical classifications. TSS is a quantification method to score the severity of inflammation on CT images based on summing up degree of acute lung inflammation lesions involvement of each lobe (including ground-glass opacity or consolidation or other fuzzy interstitial opacities) (8, 9) . To our knowledge, this is the first study that analyse TSS of chest CT and Ct values of SARS-CoV-2 RNA in both hospitalised and outpatients.

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The study protocol was approved by the Institutional Review Board and the Ethics Committee of Marmara University Faculty of Medicine.

Patients >18 years old with definitive COVID-19 diagnosis between March 22 and May 20, 2020 were included. Patients without a chest CT within 72 hours of RT-PCR positivity was excluded. Patient demographics, data regarding the in-hospital mortality and transfer or admission to ICU was collected manually from electronic health records. Information was transferred to an electronic database. A trained team of doctors reviewed the data. The first available Chest CT were recorded in patients with multiple imaging.

Diagnosis of COVID-19 infection: Turkish Ministry of Health diagnostic guideline defines a POSSIBLE case as a patient with acute respiratory illness (fever and at least one signs/symptoms of respiratory disease, e.g., cough, shortness of breath) with either a history of travel to a location reporting community transmission of COVID-19 disease or having been in contact with a confirmed COVID-19 case in the last 14 days prior to symptom onset; or a patient with severe acute respiratory illness requiring hospitalization without an alternative diagnosis that fully explains the clinical presentation. DEFINITIVE case is defined as PCR positivity is confirmed by laboratory. and severe (11) (12) (13) (14) (15) (16) (17) (18) (19) (20) . All CT images were separately evaluated by two radiologists with 3 and 4

year experiences and a consensus was reached on the final score. In cases where a consensus was not possible, a chest radiologist with 20 years of experience had the final word. (8) (9) (10) . Statistics: Descriptive statistics were presented as percentages and medians (IQR) in data without normal distribution. We compared categorical variables using the Chi-square and Fisher's exact tests. We used the Mann Whitney U test to compare continuous variables for independent groups. All tests were two-tailed; P values of < 0.05 were considered to indicate statistical significance. Statistical analyses were performed by using SPSS version 21.0 (SPSS Inc., Chicago, IL, USA).

Hospital during 22-March-2020 and 20-May-2020 were analysed. A total of 103 adult patients whose chest CT were not available at the time of positive RT-PCR assay and 61 children were excluded. After exclusion of these patients, 730 patients were available for analysis. Figure 2 shows the flowchart of our study. Thirty nine percent of the patients (n: 284) were hospitalized and 27 of them died during the hospitalization period.

Characteristics of patients were given in Table 1 . Median age was 42 years (30-55) and 365 (49.9%) were female. No significant difference was detected for the presence of fever, cough, dyspnea and contact with documented or suspected case between hospitalized and outpatiens.

In 62.3% of hospitalized patients and in 17% of outpatients there was at least one comorbidity (p<0.01). In 8.5% of hospitalized patients there were more than 3 comorbidities Compared to hospitalized patients, proportion of outpatients with high (7.0% vs 4.6% respectively) and medium (68.8% vs 59.9% respectively) nasopharyngeal viral load was significantly higher (Table 1) Table 2 ). In outpatient group severe involvement of chest CT was not observed. Viral load was significantly higher in patients with no chest CT lesions compared to patients with mild and severe chest CT involvement (Table 3) . A linear increase in median age in both inpatient and outpatients was detected, and CT severity was related with age (p<0.01) ( Table 2 We included not only hospitalised patients but also outpatients who were treated at home. We analysed the cardinal symptoms such as fever, cough and dyspnea in two groups and found no difference. The presence and the number of comorbidities were higher in hospitalized patients (p<0.01). Huang et al (14) reported that elevated CRP was associated with an increased composite poor outcome and disease severity in COVID-19. In our group, CRP levels at the time of PCR request were mostly available for hospitalized patients and a statistical comparison could not be made. In a series of 76 patients, Ct values of severe cases was shown to remain significantly lower for the first 12 days after onset than those of corresponding mild cases (15) .

However, in another study that 414 swabs collected from 94 patients high viral loads were J o u r n a l P r e -p r o o f detected soon after symptoms onset there was no difference in viral load across disease severity (16) . In our group, the mortality rate was 9.5% among hospitalized patients and viral load was not associated with mortality whereas older age, CRP positivity and CT severity were value was significantly higher in the incubation period than that of hospitalization period. Zou et al (19) showed that the viral loads were equally high among asymptomatic patients and those with symptoms which suggests the transmission potential of asymptomatic or minimally symptomatic patients. These findings are in concordance with our findings reports that in 338 of 446 outpatients there was a considerable amount of virus (high to medium) in their nasopharynx that makes them contagious to their contacts.

Chest CT as an important method for COVID-19 diagnosis has been widely used for screening, comprehensive evaluation, and following-up of patients. When chest CTs of 121 symptomatic patients infected with COVID-19 from four centers were evaluated, in the early phase (0-2days) 56% of chest CT were normal while 100% of RT-PCR were positive with a longer time after the onset of symptoms (20) . Frequency of CT findings has been suggested to be related to infection time course. Pan et al that demonstrated preponderance of ground-glass abnormality in early disease, followed by development of crazy paving, and finally increasing consolidation later in the disease course (21) . They claimed that chest CT display high specificity but low sensitivity mainly in patients presenting within the first 4 days of the disease.

In a review assessing 641 search results, the clinical utility of chest CT was reported as limited, particularly for patients who show no symptoms and patients who are screened early in disease progression (7) . Authors reported that CT sensitivity and specificity for COVID-19 was low and it should be considered a supplemental diagnostic tool, particularly for symptomatic patients. The most prominent finding in our study was the inverse relation of viral load and chest CT TSS. Viral load of samples taken from nasopharynx was significantly lower in patients who had severe lesions in CT in both outpatients and hospitalized patients. CT severity was related with age and older patients had higher severity score (p<0.01). Presence of any comorbidity was related with hospitalisation but not found to be related with CT severity. We may speculate that although viral load of SARS CoV-2 in nasopharyngeal swab specimens is high in early phase of COVID-19 it is not necessarily related with changes in chest CT. In the later phase SARS CoV-2 viral load of nasopharyngeal swab specimens decreases while that of lower respiratory tract samples is increasing and chest CT changes become detectable. In this stage, a sputum sample or other lower respiratory tract specimens could be more reliable than nasopharyngeal swab samples. Scoring of chest CT that we used is a reliable method for COVID 19 diagnosis and we may also suggest that serial scoring of repeated CT could be important for patients follow up. Further studies that combine detailed clinical analysis, RT-PCR results and CT images could confirm our suggestion.

We agree with Farfour et al's suggestion that infection prevention and control should be implemented in all suspected patients on the basis of epidemiological, clinical, or radiological findings and these measures should be stopped only when the diagnosis is excluded (22) . In our study nasopharyngeal viral load was inversely associated with the severity score of chest CT on admission. This association was present both in hospitalized patients and outpatients. We 12 suggest that, viral load is important to detect in the early stages of Covid-19 infection to minimize potential spread, whereas CT can help identify cases requiring extensive medical care.

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Acknowledgements  The study protocol was approved by the Institutional Review Board and the Ethics Committee of Marmara University Faculty of Medicine.

 The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

 There is no organizations that funded this paper J o u r n a l P r e -p r o o f J o u r n a l P r e -p r o o f J o u r n a l P r e -p r o o f Fig. 1 a-f Forty-three year old female patient admitted with ongoing fever, cough, and dyspnea for eight days. Chest CT on admission shows bilateral subpleural multifocal ground-glass opacities and consolidations with lower lobe dominance typical for SARS-CoV2 pneumonia. TSS was calculated as 10. Fig. 1 a-f Forty-three year old female patient admitted with ongoing fever, cough, and dyspnea for eight days. Chest CT on admission shows bilateral subpleural multifocal ground-glass opacities and consolidations with lower lobe dominance typical for SARS-CoV2 pneumonia. TSS was calculated as 10.

1a J o u r n a l P r e -p r o o f 

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Table 4: Factors associated with in hospital mortality in hospitalized patients. Survivors (n: 257) Deaths (n: 27) P value Age, median, (IQR)