key: cord-0886891-1ro10ujr
authors: Alpaydin, Aylin Ozgen; Gezer, Naciye Sinem; Simsek, Gokçen Omeroğlu; Tertemiz, Kemal Can; Kutsoylu, Oya Ozlem Eren; Zeka, Arzu Nazli; Guzel, Irmak; Soyturk, Mujde; Sayiner, Ayca Arzu; Oguz, Vildan Avkan
title: Clinical and Radiological Diagnosis of Non‐SARS‐CoV‐2 Viruses in the Era of Covid‐19 Pandemic
date: 2020-08-08
journal: J Med Virol
DOI: 10.1002/jmv.26410
sha: e9c5edae578ba4a0c4dc40907632368d613ec2c5
doc_id: 886891
cord_uid: 1ro10ujr

INTRODUCTION: Following the announcement of first coronavirus disease 2019 (COVID‐19) case on March 11, 2020, in Turkey we aimed to report the co‐infection rates, and the clinical, laboratory, radiological distinctive features of viral pneumonia caused by viruses other than severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). METHODS: A cross‐sectional study was conducted between 18 and 31 March 2020. COVID‐19 suspected cases admitted to pandemic policlinic who had nasopharyngeal swab specimens tested for both SARS‐CoV‐2 and other respiratory viral pathogens were included. RESULTS: Within 112 patients SARS‐CoV‐2 was detected in 34 (30%). Among the non‐SARS‐CoV‐2 viruses (n=25, 22%), metapneumovirus (n=10), was the most frequent agent. There were two co‐infections with SARS‐CoV‐2. Sputum was less in the SARS‐CoV‐2 group (p=0.003). The leukocyte, lymphocyte, and thrombocyte count and C‐reactive protein levels were lowest in the SARS‐CoV‐2 group (p<0.001, p=0.04, p<0.001, p=0.007 respectively). Peripheral involvement (80% vs. 20%, p=<0.001), pure ground‐glass opacity (65% vs. 33%, p=0.04), apicobasal gradient (60% vs. 40%, p=0.08), involvement of ≥3 lobes (80% vs. 40%, OR:6.0, 95%CI,1.33‐27.05, p=0.02) and consolidation with accompanying ground‐glass opacity (4% vs. 33%, p=0.031) were more common in SARS‐CoV‐2 group. CONCLUSION: Some clinical, laboratory and radiological findings may help in the differential diagnosis of non‐SARS‐CoV‐2 viruses from COVID‐19. However, co‐infections may occur, and a non‐SARS‐CoV‐2 pathogen positivity does not exclude accompanying COVID‐19. This article is protected by copyright. All rights reserved.

On 31 December 2019, China announced a novel coronavirus, soon named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by International Committee on Taxonomy of Viruses (ICTV), as the causative agent of these clusters of unknown pneumonia 1, 2 , which eventually evolved to a worldwide pandemic 3 .

The spectrum of SARS-CoV-2 originated human disease named as coronavirus disease 2019 (COVID- 19) changes from little to no symptoms to severe pneumonia and acute respiratory distress syndrome 4 . Gastrointestinal, cardiovascular, and musculoskeletal involvement may also occur; however, the most common presentation is respiratory symptoms like cough, shortness of breath, and fever. Nevertheless, these symptoms are highly nonspecific and may arise due to any respiratory pathogens of bacteria or viruses 5 . Such respiratory pathogens include influenza, respiratory syncytial virus (RSV), and other previously known human coronaviruses like alphacoronaviruses 229E and NL63, and the beta-coronaviruses OC43 and HKU1 as well as atypical bacteria. These may also cause mild respiratory symptoms and severe pneumonia 6 .

On March 11, 2020 , the first patient with COVID-19 was reported in Turkey.

During the following weeks, patients were evaluated according to the national definition of COVID-19, anyone with respiratory system symptoms and/or fever and history of travel abroad or contact with a confirmed COVID-19 patient within the previous 14 days, were accepted as a probable COVID-19 case. Respiratory tract specimens were collected and a diagnostic algorithm including SARS-CoV-2 reverse transcriptase PCR (RT-PCR) was performed.

On March 18, 2020 , the first COVID-19 patient was determined by a positive RT-PCR test for SARS-CoV-2 and typical symptoms in our hospital. In the meantime, other respiratory pathogens continued to be detected by the syndromic multiplex PCR assay in patients admitted to the hospital.

Reports from China demonstrated that the co-infection of SARS-CoV-2 with other respiratory pathogens were rare 7 . The confirmation of non-SARS-CoV-2 viruses may aid in the differential diagnosis of COVID-19 The Centers for This article is protected by copyright. All rights reserved.

Disease Control and Prevention also encourages testing for other respiratory pathogens in the diagnostic work of suspected COVID-19 cases 8 .

Under these conditions; it was aimed to report the co-infection rates, the prevalence, clinical, laboratory and radiological characteristics of non-SARS-CoV-2 respiratory pathogens in a teaching hospital organized as a pandemic hospital immediately at the beginning of the pandemic in Turkey.

In this retrospective cohort between 18 and 31 March, 112 COVID-19 suspected cases were evaluated. Probable COVID-19 case was defined as patients with respiratory system symptoms and/or fever and history of travel to abroad or contact with a confirmed COVID-19 patient within the previous 14 days or severe pneumonia needing hospitalization, according to the Republic of Turkey Ministry of Health guidelines, version March 11 9 . Demographic and laboratory data such as complete blood count, C-reactive protein (CRP) and procalcitonin were searched and recorded from the electronic records of the hospital database after obtaining necessary permissions and Ethical approval (No:2020/11-33, 1 st June 2020). Patients with nasopharyngeal swab specimens tested for SARS-CoV-2 and other respiratory pathogens were included.

The diagnostic testing included, upon sample receipt, a rapid molecular test for the most common respiratory pathogens as well as SARS-CoV-2 testing based on the protocol released by the World Health Organization 10 .

This article is protected by copyright. All rights reserved.

Nucleic acid extraction was EZ-1 virus mini kit using EZ-1Advanced XL platform (Qiagen). A syndromic-panel based multiplex real-time polymerase chain reaction (RT-PCR) assay was used for amplification and detection of the following human pathogens: influenza A virus, influenza B virus, rhinovirus, coronaviruses (NL63, 229E, OC43, HKU1), parainfluenza viruses 

SARS-CoV-2 RNA was tested by a one-step real-time RT-PCR assay targeting viral RdRp (Biospeedy SARS CoV-2 qPCR detection kit, Bioeksen, Turkey) provided by MoH. The test was performed on the RotorGene Q 5plex HRM. Human RNase P gene amplification was used as an internal control.

A 64-channel multidetector CT scanner (Brilliance, Philips Medical Systems) was used with an imaging protocol as follows: 120 kVp, 80 mA, slice thickness 1 mm, and high-spatial-frequency reconstruction algorithm (bone algorithm), without intravenous contrast medium. Chest CT images of all patients in axial and coronal reformate slices were evaluated by 14 years of experienced board-certificated radiologist.

All scans were reviewed for the presence and characteristics of pulmonary infiltrates. Ground-glass opacification (GGO) was defined as hazy, increased lung attenuation with preservation of the bronchial and vascular margins, and consolidation was defined as opacification with obscuration of the margins of vessels and airway walls 11 . The location of the infiltration (the right upper, middle, right lower, left upper or left lower lobes, or any combination of these), the distribution of the infiltration (peripheral, bronchocentric, central, diffuse, centrilobular, paramediastinal or any combination of these) and the presence of an apicobasal gradient in the distribution of the infiltration was recorded.

Presence of irregular reticulations, cavitation and vascular dilatation within the infiltration; the presence of crazy paving sign, reversed halo sign, tree-in-bud sign, airway changes (bronchial dilatation, bronchial wall thickening, endobronchial secretions), pleural effusion, pleural thickening, and lymphadenopathy were evaluated. A size cut-off of 15 mm short-axis diameter was used for subcarinal lymph nodes and a 10 mm short-axis diameter was used for others. CT images were also evaluated for accompanying pulmonary pathologies such as emphysema, bronchiectasis, interstitial fibrosis, pulmonary edema, and malignancy. On the other hand, non-SARS-CoV-2 viral agents, especially metapneumovirus was associated with severe pneumonia and mortality. The demographic characteristics of the study population are presented in Table I .

Among the detected respiratory viral pathogens, metapneumovirus (n=10) and rhinovirus (n=9) were the most frequent agents, each with one accompanying co-infection by other non-SARS-CoV-2 viral pathogens in single patients There were also two co-infections with SARS-CoV-2, with adenovirus and Cor NL63 reaching a total co-infection rate as 4/59 (7%) ( Table II) .

The most common clinical symptom was cough in the whole study population.

There was no significant difference in symptoms among the groups except sputum, that was the least in the SARS-CoV-2 group (p=0.003). The vital signs were similar in all groups and there was no difference between the groups in terms of heart rate, fever, and blood pressure. However, mean peripheral oxygen saturation (SpO2) of non-SARS-CoV-2 was lower than both SARS-CoV-2 and no viral pathogen groups. When laboratory data were analyzed, leucocyte, lymphocyte, and thrombocyte counts were significantly lower in the SARS-CoV-2 group (p<0.001, p=0.04, and p<0.001 respectively). This article is protected by copyright. All rights reserved.

patients had a false (+) diagnosis. Four of the patients with a false (+) diagnosis was proven non-SARS viral pneumonia (Table III) .

When chest CT findings in SARS-CoV-2 and non-SARS-CoV-2 groups were analyzed, right (80% vs. 67%) and left lower lobes (80% vs. 60%) were more commonly involved. Peripheral involvement (80% vs. 20%, p<0.001) and pure ground-glass opacity (65% vs. 33%, p=0.04) were significantly more common in SARS-CoV-2 positive group. More than three lobes involvement was two times more in SARS-CoV-2 (80%) than non-SARS-CoV-2 (40%) group (RR: 2.0, 95% CI, 1.04-3.86, p=0.379, OR: 6.0, 95% CI, 1.33-27.05, p=0.02).

Although the presence of an apicobasal gradient was more common in SARS-CoV-2 patients (60% vs. 40%) there was no significant difference between the groups (p=0.080). Consolidation with accompanying ground-glass opacity was significantly more common (4% vs. 33%) in the non-SARS-CoV-2 positive group (p=0.03) (Table IV) .

Radiological assessments for the more frequently identified Non-SARS-CoV-2 pathogens (both metapneumovirus and rhinovirus) were compatible with indeterminate or atypical for COVID-19 disease. This was also similar to mycoplasma cases. When the distribution of distinctive characteristics of pneumonic infiltration in SARS-CoV-2 and the most common identified Non-SARS-CoV-2 pathogens, reticulation was more in SARS-CoV-2 (n=10), than metapneumovirus (n=2) and rhinovirus (n=3), bronchial dilatation (n=3) and vascular enlargement (n=1) signs were only positive in SARS-CoV-2 patients.

Neither bronchial dilatation nor vascular enlargement was detected in metapneumovirus and rhinovirus pneumonia. On the other hand, atypical This article is protected by copyright. All rights reserved.

findings related to COVID-19 pneumonia such as bronchial thickening and tree in bud were only positive in metapneumovirus (n=3, n=2 respectively) and rhinovirus (n=4, n=1 respectively) (Figure 1, 2, eFigure 1-3 ).

The differential diagnosis of community-acquired pneumonia is challenging, especially when respiratory viral pathogens are also circulating in the community 13 . In this study, it was investigated features of viral pneumonia and the coinfection rates at the very early stage of the pandemic during the seasonal respiratory pathogens period in a single-center pandemic hospital in Turkey. Although SARS-CoV-2 detection had priority, non-SARS-CoV-2 viral agents were identified fairly high (n=25, 22%). The co-infection rate was 7%. group. The coinfection rates were reported between 0-20.7 % in different studies (5, 7, 14) . One study including 1206 patients showed that 9.5% of the study population was positive for SARS-CoV-2 and 26.1 % for other viruses 14 .

This article is protected by copyright. All rights reserved.

In this cohort the coinfection rates were fairly low, however, SARS-CoV-2 was the most frequently observed pathogen (30%) when compared with non-SARS-CoV-2 agents (22%). This might be due to the study period when the case rates were rapidly increasing. Metapneumovirus and rhinovirus were the most common identified agents, although influenza was expected to occur more during the period.

COVID-19 is usually mild or moderate (81%), however severe (14%) and critical illness (5%) have also been reported 15 . Patients who have mild signs and symptoms generally recover at home, however moderate or severe cases are hospitalized for observational and supportive care 16 . In this study, most of the COVID-19 patients presented with pneumonia and hospitalized significantly more to other groups. This might be due to understanding the nature of a new agent and observing the clinical progress. However, severe pneumonia and death rate was higher in the non-SARS-CoV-2 group.

Clinical signs and symptoms alone are inaccurate for the etiological diagnosis of pneumonia 17 . The most common symptoms include cough, fever, sore throat, malaise, and myalgia. All previously defined symptoms were investigated in COVID-19 and no difference was observed among the groups.

Cough and fever were the most common symptoms in all groups. However, sputum, which was not included in the clinical signs of COVID-19 in any definition, was the only identifiable symptom from other etiologies of pneumonia.

The vital signs were also similar in all groups except SpO2 which was lowest in the non-SARS-CoV-2 group. This might be related to mild This article is protected by copyright. All rights reserved.

presentation. In the laboratory data, leucocyte, lymphocyte, and thrombocyte count values were significantly lower in the SARS-CoV-2 group. Normal leucocyte counts, leukopenia, lymphopenia (80%+), thrombocytopenia has been reported in COVID-19 18 . More than half (73%) of the COVID-19 patients had increased CRP values, however, among all groups, CRP was lowest in the SARS-CoV-2 group, while procalcitonin was lowest in the unidentified etiology group. This might be due to mild inflammation at the beginning of SARS-CoV-2 and noninfectious etiologies in the unidentified etiology group. Elevated CRP, low or normal procalcitonin levels were defined as the inflammatory markers in COVID-19 19 . These results were compatible with the previous findings and we suggest that lymphopenia might be used to distinguish COVID-19 from other etiologies.

The sensitivity and specificity of chest CT in COVID-19 pneumonia have been reported as 60%-98% and 25%-53%, respectively 20 . As the widespread use of CT imaging caused increased recognition of uncommon presentations of the disease, indeterminate CT diagnosis has reached a considerable number.

The uncertainty in the management of these patients is still present. In this study, indeterminate CT diagnosis group was combined with atypical and typical for COVID-19 groups and analyzed for two options each to suggest better management of the indeterminate group. When the indeterminate CT diagnosis group was combined with the atypical for the COVID-19 group, the number of false-negative patients for SARS-CoV-2 was more (n=3) concerning the combination of indeterminate group and typical for COVID-19 group (n=1), in the cost of increased false-positive results (n=15). Therefore, it is suggested that including indeterminate CT findings in the typical group for This article is protected by copyright. All rights reserved.

not to misdiagnose COVID-19 disease during the peak stage of the pandemic.

The decision on indeterminate CT findings might be made case by case considering the course of the pandemic.

In addition to the difficulty of decision making for the indeterminate group, it is reported that typical chest CT findings of COVID-19 pneumonia may overlap with many other infections (notably viral pneumonia) and noninfectious diseases (particularly organizing pneumonia) 21 pneumonia from other viral pneumonia. However, for the group in which the etiology was not identified, false positivity (7/25) and false negativity (5/17) rates were high and CT did not help distinguish COVID-19 pneumonia. This result shows us that COVID-19 is more prone to resemble non-viral cases of pneumonia rather than viral pneumonia.

In addition to the classification of RSNA on Chest CT Findings Related to COVID-19, some clues in the differential diagnosis of pathogens that cause viral pneumonia were described previously in the literature. Viral pneumonia due to human metapneumovirus and rhinovirus have been described to show airway-centric distribution, with areas of tree-in-bud opacity and bronchial wall thickening 22 . These findings were also recognized in non-SARS-CoV-2 pneumonia.

Since consolidation obscures the reticular pattern underneath, reticulations were significantly more common in the SARS-CoV-2 group which more commonly presents with ground-glass opacity. Among the other features seen in pneumonic infiltration of COVID-19, bronchial dilation and vascular enlargement were identified in a total of four patients in SARS-CoV-2 (n=34).

Despite the small sample size of the study, it is a remarkable finding that none of the patients in the non-SARS-CoV-2 group had these findings.

In this study, it was also demonstrated that the anatomic distribution of lung lesions may also help to distinguish COVID-19 from other viral cases of pneumonia. As reported in the literature COVID-19 most commonly affects lower zones (55%), peripheral parts (87%), multifocal areas (55%) and the disease are generally quite extensive, with all five lobes being affected in 39% of patients 7, 23, 24 . All of these characteristics were more common in SARS-CoV-2 than the non-SARS-CoV-2 group of this study. Although there were no significant differences between SARS-CoV-2 and non-SARS-CoV-2 groups, the presence of an apicobasal gradient and involvement of the lower lobes may help differential diagnosis of COVID-19. Especially, COVID-19 should be considered rather than other viral cases of pneumonia if more than three lobes are involved. However, only peripheral involvement was significant in the study. This result is attributed to the small sample size of this study.

This is a single-center study, with a small number of the study population.

Another major limitation of this study was that; other reasons for respiratory This article is protected by copyright. All rights reserved.

symptoms/pneumonia in the viral pathogen negative group was not recorded. This is partly due to the limited number of specimen collections not for overwhelming the laboratory capacities, partly the small number of bacterial culture positivity even outside the pandemic.

Viral pneumonia caused by non-SARS-CoV-2 pathogens may also be present during the seasonal respiratory pathogen period. Especially metapneumovirus could be associated with severe pneumonia and mortality.

Some clinical, laboratory and especially radiological findings may aid in the differential diagnosis of non-SARS-CoV-2 pathogens from COVID-19.

However, co-infections may occur, and it should be considered that a non-SARS-CoV-2 pathogen does not exclude accompanying COVID-19. This article is protected by copyright. All rights reserved. 

Pneumonia of unknown cause-China. Geneva: WHO; 2020

World Health Organization (WHO)

Geneva: WHO; 2020

A pneumonia outbreak associated with a new coronavirus of probable bat origin

Coronavirus Disease 2019 (COVID-19)

Differential diagnosis of illness in patients under investigation for the novel coronavirus (SARS-CoV-2)

Origin and evolution of pathogenic coronaviruses

Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study

Evaluating and Testing Persons for Coronavirus Disease

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

The Role of Chest Imaging in Patient Management during the COVID-19 Pandemic: A Multinational Consensus Statement from the Fleischner Society Radiology

Radiological Society of North America Expert Consensus Statement on Reporting Chest CT Findings Related to COVID-19. Endorsed by the Society of Thoracic Radiology, the American College of Radiology, and RSNA

How recent advances in molecular tests could impact the diagnosis of pneumonia

Brown I. rates of co-infection between sars-cov-2 and other respiratory pathogens

characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of 72 314 cases from the Chinese Center for Disease Control and Prevention

All rights reserved. Accepted Article 16. Gandhi RT, Lynch JB, Del Rio C. Mild or moderate COVID-19

Diagnosis and treatment of adults with community-acquired pneumonia. An official clinical practice guideline of the American Thoracic Society and Infectious Diseases Society of America

Clinical characteristics of coronavirus disease 2019 in China

How to Deal with COVID-19 Pandemic: A Radiologic Approach

Radiological approach to COVID-19 pneumonia with an emphasis on chest CT

Radiographic and CT features of viral pneumonia

Emerging 2019 novel coronavirus (2019-nCoV) pneumonia

The authors declare no grant or financial support for the related work.

The authors declare that they have not any conflict of interest that may have influenced either the conduct or the presentation of the research.

The data that support the findings of this study are available from the corresponding author upon reasonable request. Table 3 . Chest computed tomography diagnosis of the patients according to nasopharyngeal swab molecular assay results.