Investigation of revers-transcriptase polymerase chain reaction values of patients with COVID-19 findings in lung computed tomography results

It turned out that the cause of pneumonia cases that occurred in China was due to SARS-CoV-2. The aim is to compare chest computer tomography and Revers-Transcriptase Polymerase Chain Reaction methods used in the diagnosis of COVID-19 disease with each other and to evaluate this disease with risk factors. 
The study was carried out on 66 patients. Epidemiological history, clinical symptoms, chest CT and RT-PCR results of the cases were examined. RT-PCR results of 1, 4, and 7 days were evaluated for each case with positive chest CT results. Thirty-seven of them were found to be positive on day 1, 5 of them were found to be positive on day 4, and 2 of them were found to be positive on day seven from 52 patients whose RT-PCR results were examined. In the remaining 8 cases, no positive findings were found. The most common findings are; cough (78.8%), fever (55.8%), and shortness of breath (28.8%). It was observed that 51.9% of the cases had chronic disease history and 50% of the patients using cigarettes had bilateral lung involvement in their CT results. Seven cases received intensive care support, 3 cases were intubated. Two of the intubated cases were exitus (3,8%). The positive results of RT-PCR were found to be negative in most of the cases which have positive chest CT; suggests that chest CT is more reliable in making a diagnosis.  Therefore, evaluating chest CT results with RT-PCR can be an appropriate alternative approach in the diagnosis and treatment of disease. However, in order to be fully diagnosed, the patient's history, chronic diseases, age, symptoms, imaging, blood, and test findings must all be considered as a whole.

It turned out that the cause of pneumonia cases that occurred in China was due to SARS-CoV-2. The aim is to compare chest computer tomography and Revers-Transcriptase Polymerase Chain Reaction methods used in the diagnosis of COVID-19 disease with each other and to evaluate this disease with risk factors.
The study was carried out on 66 patients. Epidemiological history, clinical symptoms, chest CT and RT-PCR results of the cases were examined. RT-PCR results of 1, 4, and 7 days were evaluated for each case with positive chest CT results. Thirty-seven of them were found to be positive on day 1, 5 of them were found to be positive on day 4, and 2 of them were found to be positive on day seven from 52 patients whose RT-PCR results were examined. In the remaining 8 cases, no positive findings were found. The most common findings are; cough (78.8%), fever (55.8%), and shortness of breath (28.8%). It was observed that 51.9% of the cases had chronic disease history and 50% of the patients using cigarettes had bilateral lung involvement in their CT results. Seven cases received intensive care support, 3 cases were intubated. Two of the intubated cases were exitus (3,8%). The positive results of RT-PCR were found to be negative in most of the cases which have positive chest CT; suggests that chest CT is more reliable in making a diagnosis. Therefore, evaluating chest CT results with RT-PCR can be an appropriate alternative approach in the diagnosis and treatment of disease. However, in order to be fully diagnosed, the patient's history, chronic diseases, age, symptoms, imaging, blood, and test findings must all be considered as a whole.
This is an open-access article under the CC-BY-SA license.

INTRODUCTION
Coronaviruses are enveloped, positive-polarized, single-stranded RNA viruses from the Coronoviridia family and their etiological agent is SARS-CoV, which previously appeared in China. 1 It was revealed that the cause of pneumonia cases occurring in Wuhan city of Hubei province of China in December 2019 was caused by SARS-CoV-2, a new species belonging to the SARS-CoV family. 2 The World Health Organization (WHO) has declared this disease called COVID-19 and originating from SARS-CoV-2 as "International Public Health Emergency". 2 Later, WHO declared the COVID-19 outbreak on Mar 11, 2020, as a pandemic due to its alarming spread around the world. 3 COVID-19 still maintains its effect in 202 countries with serious mortality rates. 4 Coronaviruses (CoV) are a large family of viruses that lead to symptoms that can progress from the common cold to severe illnesses leading up to death. 5 This new coronavirus, called SARS-CoV-2, is a new strain that has not been previously identified in humans and is thought to be due to bat. 6 Common symptoms of COVID-19 disease caused by this zoonotic virus include fever, cough, and shortness of breath. 7 In addition, symptoms such as weakness, muscle aches, sputum, hemoptysis, anorexia, nausea, vomiting, diarrhoea, and abdominal pain are also encountered. 8,9 In recent studies, it is stated that symptoms such as taste, smell loss 10 and conjunctivitis may be due to this virus. 11 There is no protective and therapeutic vaccine or specific antiviral drug for COVID-19 disease yet. The treatments are symptomatic, and oxygen therapy is applied to patients with severe signs of infection. While mechanical ventilation may be necessary in cases of resistant respiratory insufficiency, hemodynamic support is essential in the cases with septic shock. Although any antiviral therapy has not been approved; Various medications such as lopinavir/ritonavir (400/100 mg in 12 hours), chloroquine (500 mg in 12 hours), and hydroxychloroquine (200 mg in 12 hours) are recommended. Alpha-interferon (for example, 5 million units with aerosol inhalation, twice a day) is also used in treatment. 12 In addition, vitamin C, 13 vitamin D, 14 plasmapheresis, immunotherapy, 15 and even stem cells are considered among the treatment options. 16 COVID-19 is more severe in chronic patients such as old age, cardiovascular disease, diabetes mellitus, chronic respiratory diseases, hypertension, and cancer. 6 In addition, obesity and smoking affect the course of the disease negatively. 17 Smoking cessation is thought to be important in reducing viral contamination and the severity of the disease. 18 The SARS-Cov-2 virus, which is a COVID-19 agent, is transmitted from person to person through respiratory droplets, close contact, and touching the infected surfaces. Among the methods of protection from this disease, which the incubation period ranges from 2 days to 14 days, are avoiding non-compulsory travel, early diagnosis, and isolation of patients, attention to social distance, attention to hand, respiratory and environmental hygiene. 19 Viruses can be found in any environment, so it is difficult to keep our environment clean at all times. In recent studies, researchers are working on ultraviolet devices to solve this problem. In this respect, researchers think that these rays will inactivate the SARS-Cov-2 virus, based on the past literature data and the effect of UV rays on similar viruses. 20 The current method recommended by WHO in the diagnosis of Covid-19 disease is RT-PCR. The detection of SARS-Cov-2 nucleic acid by RT-PCR test from the throat swab sample taken constitutes the standard diagnostic test. In addition, chest CT is used to diagnose COVID-19 disease in the early stages as a supporter. 21 Abnormal lung tissue (83%), ground-glass opacity (73%), lung consolidation (27%), and pleural effusion (11%) are among the most common chest CT findings. 9 The aim of this study is to compare the results of chest computer CT and RT-PCR methods used in the diagnosis of COVID-19 disease and to evaluate this disease together with risk factors.

MATERIAL AND METHOD
This is a retrospective study performed with 66 cases diagnosed with COVID-19 in Siirt state hospital and whose treatment was completed. Fourteen cases of these cases with negative Computerized Tomography results were excluded from the study. Epidemiological history, clinical symptoms, Computed Tomography (CT), and Revers-Transcriptase Polymerase Chain Reaction (RT-PCR) results were evaluated.
All Chest CT images were examined by the radiologist, and the decision was made based on positive or negative CT findings. Positive CT results were grouped as unilateral lung involvement (mild involvement), bilateral lung involvement (moderate involvement), and bilateral severe lung involvement (severe involvement). RT-PCR results of the patients, who have COVID-19 findings at their Chest CT results, were evaluated at regular intervals, and the cases were grouped (Figure 1). The data obtained in the study were analyzed using SPSS (Statistical Package for Social Sciences for Windows 22.0) program. Number, percentage, average, and standard deviation were used as descriptive statistical methods in the evaluation of the data.

RESULTS AND DISCUSSION
In the study, a total of 52 cases, 27 males and 25 females diagnosed with COVID-19, were examined. The cases were divided by gender and age group (Table 1). There were Cough in 41 cases (78.8%), fever in 29 cases (55.8%), shortness of breath in 15 cases (28.8%), headache in 9 cases (17.3%), muscle pain in 9 cases (17.3 %), there were symptoms of nausea and vomiting in 1 female case. It was found that all cases with diabetes mellitus (DM), hypertension (HT), pulmonary disease (PD) were over 40 years old, and all cases with cardiovascular disease (CVD) were over 50 years old. In addition, two females had both DM and HT, and one female had DM, HT, and PH (Table 2). It was determined that 20 cases (38.4%) had no chronic illness and did not smoke. Considering the CT results of these cases, 3 cases had bilateral lung involvement (moderate involvement), and 17 cases had unilateral lung involvement (mild involvement). Two of the cases with moderate involvement were male (21 and 41 years old), and 1 was female (43 years old). It was found that these patients generally applied to the hospital late. It was observed that 18 male cases (34.6%) were smokers (7 cases using for 1-9 years, 7 cases using for 10-19 years, 4 cases using for more than 20 years). Considering the CT results of these cases, 6 cases (33.3%) were unilateral lung involvement (mild involvement), 9 cases (50%) were bilateral lung involvement (moderate involvement), and 3 cases (16.7%) were bilateral severe lung involvement (severe involvement). Unilateral lung involvement (mild involvement) in the CT of 25 cases (11 males 14 females), bilateral lung involvement (moderate involvement), in CT of 20 cases (11 males nine females), bilateral severe lung involvement in 7 cases (five males two females) was present. It was observed that cases with bilateral severe lung involvement in their CT had either smoking or chronic disease, and all were over the age of 40.
It was determined that RT-PCR results in 52 cases were positive in 37 cases and negative in 15 cases on Day 1, positive in 5 cases and negative in 10 cases on day 4, positive in 2 cases, and the remaining 8 cases were negative on day 7. It has seemed that 6 cases with negative results were mild involvement, and 2 cases with moderate involvement in the result of CT of the cases which are determined as negative (Table 3). 7 cases of 52 cases (13.4%) received intensive care support, and 3 cases (5.8%) were intubated. Two of the intubated cases were exitus (3.8%), and one was extubated. The other 4 cases were referred to the service after the intensive care treatments were finished. The first exitus case is a 49year-old male with pulmonary disease and smoking. The second exitus 42-year-old male did not have a chronic disease, was a smoker. Since December 2019, a new outbreak of coronavirus (COVID-19; previously known as 2019-nCoV) has appeared in the world. 1,6 The rapidly increasing number of cases suggests that the virus is transmitted from person to person and is more contagious than SARS-CoV and MERS-CoV. It was reported that this disease, which caused a pandemic, caused advanced alveolar damage and respiratory insufficiency. 1,22 It was stated in the studies conducted that the majority of the cases were male in the 30-69 age group, 23,24,25 and in a different study, they were male again between the ages of 39-55. 21,26 We found that the majority of cases were in the 20-29, 40-49 age groups, and men. Although it is stated in the literature studies that the average age is high, it was seen that the average age was lower in our study. It is known that asymptomatic children and adolescents make it difficult to control the outbreak. 27 For this reason, we think that children and adolescents should be evaluated among risk factors.
The most common symptom of the disease is indicated as fever; the most important symptoms after fever are cough, shortness of breath, sputum removal, myalgia, headache, hemoptysis, diarrhoea, and nausea. 1,24,25,28 Although similar symptoms were observed in our study, as different, the most common symptom was cough.
It is stated in the cases where the virus is severe and has a high mortality rate, that the average age is older, and most of them are chronic patients. 23,28,29 DM, HT, CVD, and PD are the most common chronic diseases 2,24,25,26,30,31 (Table 4). In our study, it was seen that most patients were with HT that support the literature. We think that this virus, which is pandemic nowadays, where chronic diseases are common, will increase the morbidity and mortality rates. In addition, it was observed that 20 cases (38.4%) had no chronic illnesses and did not smoke, and their CT results were positive. It is known that these patients were late for admission to the hospital. Early diagnosis and treatment, as with any disease, will reduce possible complications in the COVID-19 outbreak. Cigarette exposure, inflammatory processes in the lung, increased mucosal inflammation, expression of inflammatory cytokines and tumour necrosis factor α (TNF-α), increased permeability of epithelial cells, excessive mucous release and impaired mucociliary clearance. 32 Besides, it is known that cigarette exposure is a major risk factor for lung diseases, 32 and bacterial and viral infections are more common in smokers. 33 Studies have reported that chest CT findings and prognosis in COVID-19 patients who smoke are more severe than non-smoking patients. 34 In a similar study, the rate of smoking was found to be significantly higher in the group with the progressive disease compared to the stable group (p <0.05). 4 In our study, it was observed that smoking was higher than the literature 2,24,31 (Table  4), and 33.3% of them were mild involvement, 50% were moderate involvement, and 16.7% were heavy involvement when the CT findings of the cases were analyzed. In addition, two of the ex-patients were smoking. Consequently, the prognosis of the disease and chest CT findings are affected negatively in COVID-19 patients who smoke.
Since there is no vaccine and a specific drug developed for COVID-19 disease yet, early diagnosis and rapid isolation of patients from the community is very important. The main methods to diagnose the disease are RT-PCR, and chest CT could be to be an alternative. Several studies have also indicated that chest CT is more effective than RT-PCR test in the diagnosis of COVID-19. 21,35 In a study that is made on 1014 patients who admitted to the hospital with suspicion of COVID-19, the diagnosis rates were found to be 59% reliable for RT-PCR and 88% reliable for CT. 35 In our study, the first RT-PCR tests performed in 71.2% of patients whose chest CT findings were compatible with COVID-19 were positive. This result suggests that CT is more reliable than RT-PCR in the diagnosis of COVID-19.
In this study, as of the 7th day, the RT-PCR negativity rate of patients admitted to the hospital with suspicion of COVID-19 was 15.4%. 75% of these cases were evaluated as a mild involvement of CT. Negative results of RT-PCR may be caused by low sensitivity, improper sample intake from throat swabs, disruptions during transport, and poor performance of kits. This situation leads to delay in diagnosis and treatment, infection of a large number of people, deterioration of the prognosis of the disease, an increase in mortality, and morbidity. Therefore, evaluating chest CT results with RT-PCR can be an appropriate alternative approach in the diagnosis and treatment of disease.
Another important issue in the effective fight against epidemics such as COVID-19 is the protection of health workers from the illness at the highest level. As a matter of fact, in the COVID-19 outbreak, which we are in, health workers and other personnel working in the health sector face the risk of disease. 36 This situation creates life-threatening risks for healthcare professionals and their families, as well as other healthy individuals who apply to hospitals. Therefore, the contamination risks that may arise during the application and transportation process of RT-PCR tests should also be taken into consideration. The problems that have been experienced recently during the Ebola epidemic 'sampling and transfer' process can be shown as an example of this. 37 To prevent these problems; it may be useful to use the CT method in diagnosis.

CONCLUSION
In the diagnosis of COVID-19, it is difficult to say that a single method is sufficient. For this reason, we think that it is more accurate to evaluate the patient's history, chronic diseases, age, symptoms, CT images, laboratory and RT-PCR test results as a whole.

DISCLOSURE STATEMENT
The authors declare that they have no conflict of interest.

ACKNOWLEDGEMENT
Thank you very much for people who are helping to write this paper, especially to university.