key: cord-1032767-r0qntwbc authors: Janbabaei, G.; Brandt, E. J.; Golpira, R.; Raeisi, A.; Sadegh Tabrizi, J.; Safikhani, H. R.; Talebian, M. T.; Mirab Samiee, S.; Biglar, A.; Malekzadeh, R.; Mani, A. title: The Utility of rRT-PCR in Diagnosis and Assessment of Case-fatality rates of COVID-19 In the Iranian Population. Positive Test Results are a Marker for Illness Severity date: 2020-05-05 journal: medRxiv : the preprint server for health sciences DOI: 10.1101/2020.04.29.20085233 sha: 74f6313a253eaa8406c5d653bf5e82525df788ca doc_id: 1032767 cord_uid: r0qntwbc The utility of PCR-based testing in characterizing patients with COVID-19 and the severity of their disease remains unknown. We performed an observational study among patients presenting to hospitals in Iran who were tested for 2019-nCoV viral RNA by rRT-PCR between the fourth week of February 2020 to the fourth week of March 2020. Frequency of symptoms, comorbidities, intubation, and mortality rates were compared between COVID-19 positive vs. negative patients. 96103 patients were tested from 879 hospitals. 18754 (19.5%) tested positive for COVID-19. Positive testing was more frequent in those 50 years or older. The prevalence of cough (54.5% vs. 49.7%), fever (49.5% vs. 44.7%), and respiratory distress (43.0% vs. 39.0%) but not hypoxia (46.9% vs. 56.7%) was higher in COVID-19 positive vs. negative patients (p<0.001 for all). More patients had cardiovascular diseases (10.6% vs. 9.5%, p<0.001) and type 2 diabetes mellitus (10.8% vs. 8.7%, p<0.001) among COVID-19 positive vs. negative patients. There were fewer patients with cancer (1.1%, vs. 1.4%, p<0.001), asthma (1.9% vs. 2.5%, p<0.001), or pregnant (0.4% vs. 0.6%, =0.001) in COVID-19 positive vs. negative groups. COVID-19 positive vs. negative patients required more intubation (7.7% vs. 5.2%, p<0.001) and had higher mortality (14.6% vs. 6.3%, p<0.001). Odds ratios for death of positive vs negative patients range from 2.01 to 3.10 across all age groups. In conclusion, COVID-19 test-positive vs. test-negative patients had more severe symptoms and comorbidities, required higher intubation, and had higher mortality. rRT-PCR positive result provided diagnosis and a marker of disease severity in Iranians. follow-ups or referral to specialized centers. Those deemed as high risk for acquiring the disease, including those with T2D and hypertension, obesity, immunodeficiency, malignant disorders undergoing immune suppressive therapy, and pregnant women were prioritized. At the specialized health-care centers patients with severe respiratory distress and/or oxygen saturation below 93%, reduced levels of consciousness, or intractable cough were sent to COVID-19 referral hospitals for hospitalization. All hospitalized positive patients were put on a triple therapy treatment protocol that included Hydroxychloroquine (400 mg loading dose, followed by 200 mg twice a day), Lopinavir-Ritonavir (Kaletra), and Ribavirin for 2 weeks. Hemodynamically stable patients with mild symptoms were placed on Hydroxychloroquine and discharged to home quarantine. All data were entered into a computerized database at the National MOH COVID-19 Database. Diagnosis of COVID-19 was made based on the presence of viral RNA by real-time reverse-transcriptasepolymerase-chain-reaction (rRT-PCR) assays in accordance with the protocol established by the WHO[2] at the Pasteur Institute of Iran and at the National Reference Laboratories. Data extracted includes clinical symptoms or signs, comorbidities, ventilator use, and mortality. Radiologic assessments included computed tomography (CT) of the chest, which were not available at the time of preparation of this manuscript. Symptoms or signs included cough, fever, respiratory distress, hypoxia, myalgia, and reduced level of consciousness. Fever was defined as a forehead temperature >37.6°C. Hypoxia was defined as oxygen saturation (PO 2 ) <93%. Reduced level of consciousness was defined as reduced levels of responsiveness to verbal and noxious stimuli from obtundation to coma. Presence of other symptoms, including shivering, loss of smell (anosmia) and taste (ageusia), abdominal pain, nausea, and vomiting were documented by some centers but not systematically inquired. Comorbidities include Type 2 diabetes mellitus(T2D), cardiovascular disease, acute kidney injury, asthma, currently pregnant, chronic renal failure, cancer, and history of HIV/AIDS. Type 2 diabetes mellitus (T2D) was defined as fasting blood glucose >126 mg/dl or use of oral glycemic mediations or insulin. Cardiovascular disease was defined as history of known coronary artery disease by catheterization, history of congestive heart failure according to diagnosis codes, or ejection fraction less than 45%. Acute kidney injury was defined as a drop in glomerular filtration rate (GFR) of 25%. Chronic kidney disease was defined as GFR <60 mL/min/1.73 m 2 . Cancer is defined as active malignancy. Data on the number HIV positive or cancer patients on active therapy is not available. Intubation was defined as requiring use of a ventilator at any time during hospitalization. Mortality was defined by in-hospital death. The study was initiated by The Deputy for Health and Curative affairs at the Iranian Ministry of Health and Medical Education (MOHME) and approved by the institutional review boards of the participating hospitals (http://ethics.research.ac.ir/IndexEn.php). Data collection and analysis was supervised by the Department for All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020 . . https://doi.org/10.1101 /2020 Research and Innovation Ministry of Health and Medical Education, Tehran, Iran. The authors have reviewed the data and the manuscript and attest to the accuracy of the data and the adherence to the protocols of the NEJM.org. Comparisons between COVID-19 positive to negative patients were made using odds ratios. Cells containing <5 counts were excluded from odds ratio calculations. Comparisons between groups were made using χ 2 test or Fisher Exact test (when any cell contained <10 samples). A 2-tailed p-value <0.05 was considered statistically significant. We conducted data analysis March through April 2020. Data were analyzed using Excel v16.35 (Microsoft) and Stata 16 (StataCorp, LLC). A total of 96103 individuals were hospitalized with acute respiratory illness. 18754 (19.5%) tested positive for SARS-CoV-2 by rRT-PC (Table 1; see Supplementary Table 1 for cases by province). The mean age of COVID-19 positive and COVID-19 negative patients were 55.2 and 50.9 years, respectively. There were more men than women among COVID-19 positive patients (61% vs. 39%). Among children under 10 years and 10 to 20 years, 3.6% and 6.8% were COVID-19 positive, respectively ( Table 1 ). The percent positive increased to 11.3% and 17.4% in subjects 20-30 and 30-40 years old, respectively. Above age 40, positive results were present in about 20% of cases (range: 20.8% to 22.3%). A total of 52666 (54.8%) of the 96103 hospitalized patients were discharged home. 10277 (19.5%) of these 52666 patients were COVID-19 positive (Supplementary Table 1) . COVID-19 positive patients showed higher incidence of cough, fever, respiratory distress, and myalgia (Table 2, Fig. 1 ). Whereas, there was a lower incidence of hypoxia and reduced level of consciousness. Directionality of symptoms was similar across all age groups, although differences between COVID-19 positive vs. negative patients were less apparent in the age groups <20 years old (Fig. 1) . Additionally, as age increased the frequency of cough, fever, hypoxia decreased while respiratory distress tended to increase (Supplementary Table 2 ). T2D and cardiovascular diseases were the two major comorbidities more prevalent among COVID-19 positive compared to COVID-19 negative patients with acute respiratory disease (Table 2. Fig. 1, Supplementary Table 3 ). There were no significant differences in the rate of HIV/AIDS, chronic kidney disease, chronic anemia, acute kidney injury, hemodialysis treatment and congenital diseases between the two groups. Strikingly there were fewer patients with asthma, cancer, or pregnancy in COVID-19 positive compared to COVID-19 negative patients (Table 2 . Fig. 1 ). A total of 1450 (7.7%) COVID-19 positive and 3999 (5.2%) COVID-19 negative individuals received ventilatory support (p<0.001) (Supplementary Table 4) , which translates to an absolute difference of 26% (Table 2 , Fig 2) . There were higher number of COVID-19 positive vs. negative patients requiring ventilatory support in all age groups. All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020 . . https://doi.org/10.1101 /2020 Frequency of death was higher among COVID-19 positive (n=2740, 14.6%) vs. COVID-19 negative patients (n=4898, 6.3%) ( Table 3) . The odds ratios for death for COVID-19 positive vs. negative patients was higher across all age groups (Table 3 and Fig. 2 ). An urgent collaborative response from multiple Iranian agencies resulted in a rapid symptom screening of a large portion of the country's population. Among these about 100,000 cases of concern were identified, about 1-in-5 of whom were tested positive for COVID-19 with rRT-PCR. Notably, cases that were COVID-19 positive were more likely to have cough, fever, respiratory distress, and myalgia, but lower level of hypoxia. Positive cases were also more likely to have cardiovascular disease or T2D but less likely to have asthma, cancer, or be pregnant. COVID-19 testing was associated with increased odds for intubation of 1.5 and death of 2.5 times compared to those with negative testing. The pandemic of COVID-19 has caused devastation in many countries and continues to spread throughout the world. The early diagnosis of the disease in the population is the most efficient way to prevent further spread of this disease and is a necessary step toward its eradication. To this date several types of testing have been generated but none have been perfect. 93%), the method is not practical in normal settings and is associated with high risk of disease transmission to the health care providers. At this point rRT-PCR of the virus RNA from nasal swabs remain the most practical way for diagnosis of the disease. Therefore, we examined its utility in disease diagnosis and as a marker of disease severity in more than 90,000 suspicious cases in Iran. By comparing signs and symptoms and complications of COVID-19 test positive patients with those negative for the test we demonstrate here the utility of this test as a marker of disease severity. Those positive for COVID-19 in our study had differential symptoms compared to COVID-19 negative cases. One would expect that COVID-19 patient would be more likely to present with all viral type symptoms. This was mostly true in our study. However, in opposition to previous reports[4], oxygen desaturation was not more common among COVID-19 positive vs. negative patients. Instead, other clinical findings of fever, cough, and respiratory distress were associated with positive testing. This suggests that hypoxia should not be the only symptom that increases clinician suspicion for COVID-19 Those positive for COVID-19 in our study were more likely to have cardiovascular disease, diabetes, and had higher rates of intubation and death compared to COVID-19 test-negative patients. This may reflect greater virus replication and higher viral load in severe cases as previously shown [5] , which expectedly results in easier detection of viral genome and increased disease severity. Interesting, the rates of intubation and death were higher in COVID-19 test-positive vs. test-negative patients in all age groups, including children and adolescents. Earlier studies from China had shown higher rate of disease and its complications among patients older than 65[6]. Our data indicates that COVID-19 has disproportionately affected young individuals in Iran All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. . https://doi.org/10. 1101 /2020 compared to other countries. This may reflect the unique population structure of Iran, which is significantly younger compared to most other countries (World Population Prospects 2019, https://population.un.org/wpp/). In addition, limited access to study drugs and modern therapies due to the economic sanction may have partially accounted for the increased death rate in the younger generations [7] . High prevalence of T2D and metabolic syndrome in Iranians youth may have also increased susceptibility to disease and its complications. [8] Accordingly, there were more patients with T2D in COVID-19 test-positive vs. negative groups. An association between T2D and poor outcome in patients with COVID-19 has been previously reported [9, 10] . Our data also identifies cardiovascular disease as a comorbidity that increases the susceptibility to COVID-19. One intriguing finding of our study is the reduced number of patients that are COVID-19 test positive among those with HIV/AIDS, asthma, cancer, and pregnant women. Based on data from the trials of antiretroviral therapy in Adults Hospitalized patients with severe it is unlikely that HIV patients benefited from antiretroviral drugs. It has been hypothesized that a subgroup of patients with severe COVID-19 might suffer from cytokine storm [11] . It is, therefore, more likely that impaired immune system in HIV patients reduces the frequency of cytokine storm. Alternatively, the lower disease rates among higher risk groups is due to a lower threshold for testing in these populations or an increased adherence to social distance among those with known immunocompromising diseases. Information on what percentage of the patients with cancer were being treated with immune suppressive therapy is therefore critical but lacking at this point. In addition, data on lymphocyte count, plasma CRP, IL-6 and TNF was not available when our data were compiled and is being actively collected. Undoubtedly, establishing as to whether cytokine storm underlies disease pathogenesis in severe COVID-19 can have important therapeutic implications. As with many other countries in the world, lack of experience has undoubtedly led to shortcomings and errors in facing this pandemic. However, considering the structure of the society that promotes high social contacts and many public events that have occurred since the begin of the COVID-19 pandemic mortality in Iran has been significantly lower than anticipated. One possible factor that has limited the number of deaths is the existence of a centralized health care system that has allowed health care authorities to allocate more hospitals and beds and issue uniform guidelines for therapy and use of resources for COVID-19 patients. Accordingly, in contrast to many other countries no shortage of ventilators in Iran has been encountered. Our study has limitations that confines interpretation. Our data does not include the chest CT-scan results of patients with acute respiratory illness. Access to this data given the probability of false negative PCR results is particularly important. Additionally, the data analyzed in our study were aggregated and hence adjustment for multiple covariates due to lack of access to patient level data could not be carried out. Nevertheless, the higher rate of mortality in patients tested positive vs. those tested negatives suggests that the PCR-based testing has been a relatively suitable method for the screening of high-risk patients. Our experience suggests that use of rRT-PCR diagnostic method allows better identification of high-risk patients and early utilization of advanced therapeutic measures. Lessons from Iranian experience of COVID-19 All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. . https://doi.org/10. 1101 /2020 should hopefully assist other countries in reducing the fatalities and the economic burden of this pandemic and facilitate preparedness for future pandemics. All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. . https://doi.org/10.1101/2020.04.29.20085233 doi: medRxiv preprint We would like to acknowledge all clinicians, nurses, and healthcare workers in 879 hospitals in Iran for their unlimited devotion to the care of Iranian COVID-19 patients while sacrificing their health and lives. We like to thank Dr. Saeed Namaki, the Minister of health for his leadership and dedication to the care of COVID-19 patients and Drs. Tayeb Ghadimi, and. Abdolkhalegh Keshavarzi, Mr. Reza Mahmoudi Lamouki, and Bagherzadeh for their help with the data preparation, management and analysis. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. . https://doi.org/10. 1101 /2020 was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. . https://doi.org/10. 1101 /2020 was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. . All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. . https://doi.org/10.1101/2020.04.29.20085233 doi: medRxiv preprint C: Odds ratio for COVID-19 positive vs negative patients of presenting symptoms and signs by age groups and overall B: Odds ratio for COVID-19 positive vs negative patients of presenting comorbidities by age groups and overall All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. O v e r a l l All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. . https://doi.org/10.1101/2020.04.29.20085233 doi: medRxiv preprint All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. Supplementary table 1-List of total admission for acute respiratory illness during designated month in 31 provinces of Iran and the change in number of admissions between 2 days to one day prior to the completion of the study All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020 . . https://doi.org/10.1101 /2020 Supplement was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. All rights reserved. No reuse allowed without permission. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. . https://doi.org/10. 1101 /2020 was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint (which this version posted May 5, 2020. . https://doi.org/10. 1101 /2020 Supplement Table 4: Intubation by age group, including calculations for χ 2 testing