Studying pulmonary fibrosis due to microbial infection via automated microscopic image analysis.

Introduction: Pulmonary fibrosis is a consequential complication of microbial infections, which has notably been observed in SARS-CoV-2 infections in recent times. Macrophage polarization, specifically the M2-type, is a significant mechanism that induces pulmonary fibrosis, and its role in the development of Post- COVID-19 Pulmonary Fibrosis is worth investigating. While pathological examination is the gold standard for studying pulmonary fibrosis, manual review is subject to limitations. In light of this, we have constructed a novel method that utilizes artificial intelligence techniques to analyze fibro-pathological images. This method involves image registration, cropping, fibrosis degree classification, cell counting and calibration, and it has been utilized to analyze microscopic images of COVID-19 lung tissue. Methods: Our approach combines the Transformer network with ResNet for fibrosis degree classification, leading to a significant improvement over the use of ResNet or Transformer individually. Furthermore, we employ semi-supervised learning which utilize both labeled and unlabeled data to enhance the ability of the classification network in analyzing complex samples. To facilitate cell counting, we applied the Trimap method to localize target cells. To further improve the accuracy of the counting results, we utilized an effective area calibration method that better reflects the positive density of target cells. Results: The image analysis method developed in this paper allows for standardization, precision, and staging of pulmonary fibrosis. Analysis of microscopic images of COVID-19 lung tissue revealed a significant number of macrophage aggregates, among which the number of M2-type macrophages was proportional to the degree of fibrosis. Discussion: The image analysis method provids a more standardized approach and more accurate data for correlation studies on the degree of pulmonary fibrosis. This advancement can assist in the treatment and prevention of pulmonary fibrosis. And M2-type macrophage polarization is a critical mechanism that affects pulmonary fibrosis, and its specific molecular mechanism warrants further exploration.

Analytical performance of rapid nucleic acid detection assays and routine RT-qPCR assays for detection of SARS-CoV-2 in Shanghai, China in 2022.

Diagnostic accuracy of COVID-19 varies among different assays. In this study, the analytical performance of 1 rapid nucleic acid detection assay (Coyote assay) and 2 routine RT-qPCR assays (BioGerm assay and DaAn assay) was evaluated, using 1196 clinical samples. Disagreement in the results of 2 paired targets occurred in all 3 assays. The Coyote assay failed to detect 15 samples, and the DaAn assay failed to detect 5 samples. The Cohen's kappa coefficient was 0.970 between the BioGerm and DaAn assays, 0.907 between the Coyote and BioGerm assays, and 0.936 between the Coyote and DaAn assays. The positive percent agreement, and negative percent agreement of the Coyote assay were 84.04%, and 100%, respectively. Our study revealed that the results of the Coyote, BioGerm, and DaAn assays were highly consistent, which provided reference for the application of these assays for diagnosis of COVID-19.

Structure-free antibody paratope similarity prediction for in silico epitope binning via protein language models.

Antibodies are an important group of biological molecules that are used as therapeutics and diagnostic tools. Although millions of antibody sequences are available, identifying their structural and functional similarity and their antigen binding sites remains a challenge at large scale. Here, we present a fast, sequence-based computational method for antibody paratope prediction based on protein language models. The paratope information is then used to measure similarity among antibodies via protein language models. Our computational method enables binning of antibody discovery hits into groups as the function of epitope engagement. We further demonstrate the utility of the method by identifying antibodies targeting highly similar epitopes of the same antigens from a large pool of antibody sequences, using two case studies: SARS CoV2 Receptor Binding Domain (RBD) and Epidermal Growth Factor Receptor (EGFR). Our approach highlights the potential in accelerating antibody discovery by enhancing hit prioritization and diversity selection.

Reply: SARS-CoV-2 vaccination in inflammatory bowel disease patients with different biological agents.

We thank Dr Mungmunpuntipantip and colleague for their interest and thoughtful comments on our publication. The authors have highlighted several important considerations for the impact of SARS-CoV-2 vaccination in inflammatory bowel disease (IBD) patients with different biological agents. We fully agree with the author's point of view, and we also point out the limitations in our meta-analysis.

Impact of SARS-CoV-2 vaccination in inflammatory bowel disease patients with different biological agents: a systematic review and meta-analysis.

BACKGROUND: There are concerns regarding the effect of biological agents on SARS-CoV-2 vaccination in patients with inflammatory bowel disease (IBD). A systematic review and meta-analysis was performed about the serological responses, breakthrough infections and clinical relapse of IBD patients treated with biological agents following SARS-CoV-2 vaccination. METHODS: Electronic databases were searched to identify relevant studies. Primary outcomes were the pooled seroconversion rates, breakthrough infection rates and clinical relapse rates after SARS-CoV-2 vaccination in IBD patients treated with biological agents. Secondary outcomes were the comparison of seroconversion rates, breakthrough infection rates and clinical relapse rates in IBD patients treated with biological agents and control cohort after SARS-CoV-2 vaccination. RESULTS: Thirty-five studies were included in this meta-analysis. A high percentage of seroconversion (96.6%, 99% and 99.2%) was achieved in IBD patients treated with anti-TNF-α therapy, vedolizumab and ustekinumab after SARS-CoV-2 vaccination, respectively. The pooled breakthrough infection rate was 2.5% and 3.9% in IBD patients treated with anti-TNF-α therapy and vedolizumab, respectively. The breakthrough infection rate in IBD patients treated with anti-TNF-α therapy was significantly lower than control cohort (RR 0.178, 95% CI 0.084-0.378). The pooled clinical relapse rate in IBD patients treated with anti-TNF-α therapy, vedolizumab and ustekinumab was 6.9%, 5.4% and 5.3%, respectively. CONCLUSION: The overall seroconversion rate after SARS-CoV-2 vaccination in IBD patients treated with biological agents is high. The overall breakthrough infection rate and clinical relapse rate in IBD patients treated with biological agents were low.

The economic damage of COVID-19 on regional economies: an application of a spatial computable general equilibrium model to South Korea

We developed a spatial computable general equilibrium model of South Korea to assess the spatial spillover effects of the COVID-19 pandemic on South Korea’s regional economic growth patterns. The model measures a wide range of economic losses, including human health costs at the city and county level, through an analysis of regional producers’ profit maximization on the supply side and regional households’ utility maximization on the demand side. The model’s findings showed that if the level of spatial interaction decreases by 10% as a result of social distancing policies, the national gross domestic product drops by 0.815–0.864%. This loss in economic growth can be further decomposed into 0.729% loss in agglomeration effect, 0.080–0.130% loss in health effect associated with medical treatment and premature mortality, and 0.005% loss in labor effect. The results of the models and simulations shed light on not only the epidemiological effects of social distancing interventions, but also their resultant economic consequences. This ex-ante evaluation of social distancing measures’ effects can serve as a guide for future policy decisions made at both the national and regional level, providing policymakers with the tools for tailored solutions that address both regional economic circumstances and the spatial distribution of COVID-19 cases.

Self-reported Treatment Goals in Chinese Patients with Inflammatory Bowel Disease During the Coronavirus Disease 2019 Pandemic.

BACKGROUND: Inflammatory bowel disease is a chronic recurrent disease, and the treatment goals of inflammatory bowel disease are mainly based on doctors' perspective, but there are some differences between the doctor's perspective and the patient's perspective. The aim of this study is to understand the treatment goals and the related factors from the patients' perspective during the coronavirus disease 2019 pandemic. METHODS: A total of 212 participants were recruited to fill out the questionnaires including clinical characteristics and treatment goals. Eleven treatment goals were measured by a Short-Form 34 questionnaire. Univariate and multivariate regression analyses were used to explore the related factors about these treatment goals. RESULTS: A total of 212 inflammatory bowel disease patients were enrolled in this study. The most concerned treatment goal was the improvement of quality of life (mean score was 8.54), while mean score of ulcerative colitis patients and Crohn's disease patients was 9.10 and 8.45, respectively. We had also found some related factors such as the type of disease, the course of disease, the frequency of hematochezia, and defecation. CONCLUSION: Our survey showed that inflammatory bowel disease patients pay more attention to the improvement of quality of life and few drugs during the coronavirus disease 2019 pandemic. There are some related factors such as the type of disease, the course of dis- ease, the frequency of hematochezia, and defecation. Our results help clinicians understand the patients' treatment goals, which can contribute to better management of inflammatory bowel disease patients.

Isolation of Elizabethkingia anophelis From COVID-19 Swab Kits.

Purpose: To investigate and characterize the putative Elizabethkingia anophelis contaminant isolated from throat and anal swab samples of patients from three fever epidemic clusters, which were not COVID-19 related, in Shenzhen, China, during COVID-19 pandemic. Methods: Bacteria were cultured from throat (n = 28) and anal (n = 3) swab samples from 28 fever adolescent patients. The isolated bacterial strains were identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) and the VITEK2 automated identification system. Nucleic acids were extracted from the patient samples (n = 31), unopened virus collection kits from the same manufacturer as the patient samples (n = 35, blank samples) and from unopened throat swab collection kits of two other manufacturers (n = 22, control samples). Metagenomic sequencing and quantitative real-time PCR (qPCR) detection were performed. Blood serum collected from patients (n = 13) was assessed for the presence of antibodies to E. anophelis. The genomic characteristics, antibiotic susceptibility, and heat resistance of E. anophelis isolates (n = 31) were analyzed. Results: The isolates were identified by MALDI-TOF/MS and VITEK2 as Elizabethkingia meningoseptica. DNA sequence analysis confirmed isolates to be E. anophelis. The patients' samples and blank samples were positive for E. anophelis. Control samples were negative for E. anophelis. The sera from a sub-sample of 13 patients were antibody-negative for isolated E. anophelis. Most of the isolates were highly homologous and carried multiple ß-lactamase genes (bla B, bla GOB, and bla CME). The isolates displayed resistance to nitrofurans, penicillins, and most ß-lactam drugs. The bacteria survived heating at 56°C for 30 min. Conclusion: The unopened commercial virus collection kits from the same manufacturer as those used to swab patients were contaminated with E. anophelis. Patients were not infected with E. anophelis and the causative agent for the fevers remains unidentified. The relevant authorities were swiftly notified of this discovery and subsequent collection kits were not contaminated. DNA sequence-based techniques are the definitive method for Elizabethkingia species identification. The E. anophelis isolates were multidrug-resistant, with partial heat resistance, making them difficult to eradicate from contaminated surfaces. Such resistance indicates that more attention should be paid to disinfection protocols, especially in hospitals, to avoid outbreaks of E. anophelis infection.

Lower handgrip strength levels probably precede triglyceride glucose index and associated with diabetes in men not in women.

AIMS/INTRODUCTION: To explore the relationship between handgrip strength per weight (HGS/W), triglyceride glucose index (TyG) and diabetes, and whether lower HGS levels precede TyG in the Chinese elderly population. MATERIALS AND METHODS: Two linear regression models were used to explore the association of whether baseline HGS/W predicted follow-up variation of TyG or baseline TyG predicted follow-up variation of HGS/W. The logistic regression model was used to examine the relationship between baseline HGS/W and future diabetes. RESULTS: A total of 4,561 participants in the China Health and Retirement Longitudinal Study were enrolled, of which 47.0% were men, and the mean age was 58.7 years (standard deviation 8.68 years). A lower baseline HGS/W significantly correlated with a higher level of follow-up TyG (ß = -0.173, P = 0.002). The baseline level of HGS/W was significantly negatively associated with the incidence risk of diabetes (rate ratio 0.375, P = 0.004). However, in sex stratification, the statistical association between HGS/W and TyG and diabetes was only in men. CONCLUSIONS: Our results showed that HGS/W was inversely associated with TyG and diabetes, and lower HGS/W levels preceded TyG levels in the elderly population. However, the effect was inconsistent between men and women, and the possible mechanism would require further clarification.

Epitope Profiling Reveals the Critical Antigenic Determinants in SARS-CoV-2 RBD-Based Antigen.

The ongoing COVID-19 pandemic caused by SARS-CoV-2 is a huge public health crisis for the globe. The receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein plays a vital role in viral infection and serves as a major target for developing neutralizing antibodies. In this study, the antibody response to the RBD of SARS-CoV-2 S protein was analyzed by a panel of sera from animals immunized with RBD-based antigens and four linear B-cell epitope peptides (R345, R405, R450 and R465) were revealed. The immunogenicity of three immunodominant peptides (R345, R405, R465) was further accessed by peptide immunization in mice, and all of them could induced potent antibody response to SARS-CoV-2 S protein, indicating that the three determinants in the RBD were immunogenic. We further generated and characterized monoclonal antibodies (15G9, 12C10 and 10D2) binding to these epitope peptides, and finely mapped the three immunodominant epitopes using the corresponding antibodies. Neutralization assays showed that all three monoclonal antibodies had neutralization activity. Results from IFA and western blotting showed that 12C10 was a cross-reactive antibody against both of SARS-CoV-2 and SARS-CoV. Results from conservative and structural analysis showed that 350VYAWN354 was a highly conserved epitope and exposed on the surface of SARS-CoV-2 S trimer, whereas 473YQAGSTP479 located in the receptor binding motif (RBM) was variable among different SARS-CoV-2 strains. 407VRQIAP412 was a highly conserved, but cryptic epitope shared between SARS-CoV-2 and SARS-CoV. These findings provide important information for understanding the humoral antibody response to the RBD of SARS-CoV-2 S protein and may facilitate further efforts to design SARS-CoV-2 vaccines and the target of COVID-19 diagnostic.

Epidemiological characteristics and clinical manifestations of pediatric patients with COVID-19 in China: A multicenter retrospective study.

Importance: The Coronavirus disease 2019 (COVID-19) global pandemic poses a considerable challenge for pediatricians. Objective: This study aimed to identify the epidemiological characteristics and clinical features of pediatric patients with COVID-19 in China. Methods: This multicenter retrospective study included pediatric patients from 46 hospitals in China, covering 12 provinces and two municipalities. Epidemiological, demographic, clinical, laboratory, treatment, and outcome data were analyzed. Results: In total, 211 pediatric patients with COVID-19 were included in this study. The median age was 7.0 years (range: 22 days to 18 years). Approximately 16.3% of the patients exhibited asymptomatic infections, 23.0% had upper respiratory tract infections, and 60.7% had pneumonia, including two with severe pneumonia and one with critical illness. Approximately 78.7% of the pediatric patients occurred in familial clusters. The most three common symptoms or signs at onset in children with COVID-19 were fever (54.5%), cough (49.3%), and pharyngeal congestion (20.8%). Only 17.6% of the patients presented with decreased lymphocyte count, whereas 13.6% had increased lymphocyte count. Among the patients with pneumonia who exhibited abnormal chest computed tomography findings, 18.2% (23/127) of the patients had no other symptoms. Generally, the chest radiographs showed abnormalities that affected both lungs (49.6%); ground-glass opacity (47.2%) was the most common manifestation. The cure and improvement rates were 86.7% (183/211) and 13.3% (28/211), respectively. Only one patient with an underlying condition received invasive mechanical ventilation; none of the patients died. Interpretation: Similar to adults, children of all age groups are susceptible to COVID-19. Fortunately, most pediatric patients have mild symptoms or remain asymptomatic, despite the high incidence of pneumonia. Decreased proportions of white blood cells and lymphocytes are less frequent in children than in adults.

The Association of Suicidal Ideation With Family Characteristics and Social Support of the First Batch of Students Returning to a College During the COVID-19 Epidemic Period: A Cross Sectional Study in China.

Objective: To investigate the prevalence of suicidal ideation among the first batch of students returning to a college during the COVID-19 epidemic, and to explore the correlation of suicidal ideation with family characteristics and social support. Methods: A cluster sampling survey with a self-designed questionnaire was conducted among the first batch of students returning to a college in Wuhu, China. The Positive and Negative Suicidal ideation (PANSI) and Social Support Scale (SSRS) were used to define students' suicidal ideation and social support, respectively. The influence of family characteristics and social support on the students' suicidal ideation was investigated using multivariate unconditional logistic regression analysis. Results: Two thousand seven hundred valid questionnaires were collected, including 673 males (24.9%) and 2,027 females (75.1%), in this study. A total of 146 students (5.4%) showed suicidal ideation. Male respondents reported higher rates (7.9%) than females (4.6%). Multivariate logistic regression analysis showed that a higher risk level of residence before returning to school and lower objective support were the risk factors for suicidal ideation in males. In contrast, a higher level of maternal education, a poorer relationship with the mother, and lower scores for subjective support and support availability had significant effects on females' suicidal ideation. Limitations: This is a cross-sectional study, and lacks comparison to the time point unaffected by COVID-19. Moreover, it was limited by COVID-19 epidemic prevention and control restrictions, and the differences in returning to school in different regions. Only one college was investigated in this study, and all of the respondents were sophomores, so there may be some limitations in the representativeness of the sample and extrapolation of the results. Conclusion: Family characteristics and social support have had an important influence on suicidal ideation among students returning to school during the COVID-19 epidemic. Some gender differences were identified. Targeted interventions are needed for early prevention and control.

CT Quantification of COVID-19 Pneumonia at Admission Can Predict Progression to Critical Illness: A Retrospective Multicenter Cohort Study.

Objective: Early identification of coronavirus disease 2019 (COVID-19) patients with worse outcomes may benefit clinical management of patients. We aimed to quantify pneumonia findings on CT at admission to predict progression to critical illness in COVID-19 patients. Methods: This retrospective study included laboratory-confirmed adult patients with COVID-19. All patients underwent a thin-section chest computed tomography (CT) scans showing evidence of pneumonia. CT images with severe moving artifacts were excluded from analysis. Patients' clinical and laboratory data were collected from medical records. Three quantitative CT features of pneumonia lesions were automatically calculated using a care.ai Intelligent Multi-disciplinary Imaging Diagnosis Platform Intelligent Evaluation System of Chest CT for COVID-19, denoting the percentage of pneumonia volume (PPV), ground-glass opacity volume (PGV), and consolidation volume (PCV). According to Chinese COVID-19 guidelines (trial version 7), patients were divided into noncritical and critical groups. Critical illness was defined as a composite of admission to the intensive care unit, respiratory failure requiring mechanical ventilation, shock, or death. The performance of PPV, PGV, and PCV in discrimination of critical illness was assessed. The correlations between PPV and laboratory variables were assessed by Pearson correlation analysis. Results: A total of 140 patients were included, with mean age of 58.6 years, and 85 (60.7%) were male. Thirty-two (22.9%) patients were critical. Using a cutoff value of 22.6%, the PPV had the highest performance in predicting critical illness, with an area under the curve of 0.868, sensitivity of 81.3%, and specificity of 80.6%. The PPV had moderately positive correlation with neutrophil (%) (r = 0.535, p < 0.001), erythrocyte sedimentation rate (r = 0.567, p < 0.001), d-Dimer (r = 0.444, p < 0.001), high-sensitivity C-reactive protein (r = 0.495, p < 0.001), aspartate aminotransferase (r = 0.410, p < 0.001), lactate dehydrogenase (r = 0.644, p < 0.001), and urea nitrogen (r = 0.439, p < 0.001), whereas the PPV had moderately negative correlation with lymphocyte (%) (r = -0.535, p < 0.001). Conclusions: Pneumonia volume quantified on initial CT can non-invasively predict the progression to critical illness in advance, which serve as a prognostic marker of COVID-19.

A newly identified linear epitope on non-RBD region of SARS-CoV-2 spike protein improves the serological detection rate of COVID-19 patients.

BACKGROUND: Serological test is helpful in confirming and tracking infectious diseases in large population with the advantage of fast and convenience. Using the specific epitope peptides identified from the whole antigen as the detection antigen is sensitive and relatively economical. The development of epitope peptide-based detection kits for COVID-19 patients requires comprehensive information about epitope peptides. But the data on B cell epitope of SARS-CoV-2 spike protein is still limited. More importantly, there is a lack of serological data on the peptides in the population. In this study, we aimed to identify the B cell epitope peptides of spike protein and detect the reactivity in serum samples, for further providing data support for their subsequent serological applications. RESULTS: Two B cell linear epitopes, P104 and P82, located in non-RBD region of SARS-CoV-2 S protein were identified by indirect ELISA screening of an overlapping peptide library of the S protein with COVID-19 patients' convalescent serum. And the peptides were verified by testing with 165 serum samples. P104 has not been reported previously; P82 is contained in peptide S21P2 reported before. The positive reaction rates of epitope peptides S14P5 and S21P2, the two non-RBD region epitopes identified by Poh et al., and P82 and P104 were 77.0%, 73.9%, 61.2% and 30.3%, respectively, for 165 convalescent sera, including 30 asymptomatic patients. Although P104 had the lowest positive rate for total patients (30.3%), it exhibited slight advantage for detection of asymptomatic infections (36.7%). Combination of epitopes significantly improved the positive reaction rate. Among all combination patterns, (S14P5 + S21P2 + P104) pattern exhibited the highest positive reaction rate for all patients (92.7%), as well as for asymptomatic infections (86.7%), confirming the feasibility of P104 as supplementary antigen for serological detection. In addition, we analyzed the correlation between epitopes with neutralizing antibody, but only S14P5 had a medium positive correlation with neutralizing antibody titre (rs = 0.510, P < 0.01). CONCLUSION: Our research proved that epitopes on non-RBD region are of value in serological detection especially when combination more than one epitope, thus providing serological reaction information about the four epitopes, which has valuable references for their usage.

Impact of treatment delays on vitiligo during the COVID-19 pandemic: A retrospective study.

Due to the COVID-19 pandemic, routine treatments are delayed to some extent and their negative impacts have been widely reported. However, virtually nothing is known about vitiligo in the context of COVID-19. Therefore, we analyzed treatment delays and its impact on vitiligo, aiming to provide suggestions on vitiligo management within this special period. We performed a retrospective cohort study on 322 patients who visited our clinics at least 2 times from January to December 2020, and their medical records and photographs were reviewed. Patients were divided into normal (n = 155) and late group (n = 167) based on whether experienced treatment delays. As for the active cases, the late group showed higher progression rate than normal group (35 of 86 [40.7%] vs. 10 of 81 [12.3%]; p = 0.002). Moreover, we observed higher recurrence rate in delay group than those of normal group (26 of 81[32.1%] vs. 9 of 74 [12.2%]; p = 0.018) among stable cases. Further univariate and multivariate analysis determined treatment delays as the most important independent risk factor for disease progression and recurrence, and maintenance therapy (>2 years) as a protective factor against recurrence. This study, for the first time, revealed the independent adverse impact of treatment delays on the progression and recurrence of vitiligo and indicated the significance of continuous treatment for halting progression and long-term maintenance therapy for preventing recurrence for vitiligo, which should be highly valued in the management of vitiligo during the COVID-19 pandemic.

Comparative evaluation of six nucleic acid amplification kits for SARS-CoV-2 RNA detection.

BACKGROUND: SARS-CoV-2 is a newly emerged coronavirus, causing the coronavirus disease 2019 (COVID-19) outbreak in December, 2019. As drugs and vaccines of COVID-19 remain in development, accurate virus detection plays a crucial role in the current public health crisis. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) kits have been reliably used for detection of SARS-CoV-2 RNA since the beginning of the COVID-19 outbreak, whereas isothermal nucleic acid amplification-based point-of-care automated kits have also been considered as a simpler and rapid alternative. However, as these kits have only been developed and applied clinically within a short timeframe, their clinical performance has not been adequately evaluated to date. We describe a comparative study between a newly developed cross-priming isothermal amplification (CPA) kit (Kit A) and five RT-qPCR kits (Kits B-F) to evaluate their sensitivity, specificity, predictive values and accuracy. METHODS: Fifty-two clinical samples were used including throat swabs (n = 30), nasal swabs (n = 7), nasopharyngeal swabs (n = 7) and sputum specimens (n = 8), comprising confirmed (n = 26) and negative cases (n = 26). SARS-CoV-2 detection was simultaneously performed on each sample using six nucleic acid amplification kits. The sensitivity, specificity, positive/negative predictive values (PPV/NPV) and the accuracy for each kit were assessed using clinical manifestation and molecular diagnoses as the reference standard. Reproducibility for RT-qPCR kits was evaluated in triplicate by three different operators using a SARS-CoV-2 RNA-positive sample. On the basis of the six kits' evaluation results, CPA kit (Kit A) and two RT-qPCR Kits (Kit B and F) were applied to the SARS-CoV-2 detection in close-contacts of COVID-19 patients. RESULTS: For Kit A, the sensitivity, specificity, PPV/NPV and accuracy were 100%. Among the five RT-qPCR kits, Kits B, C and F had good agreement with the clinical diagnostic reports (Kappa ≥ 0.75); Kits D and E were less congruent (0.4 ≤ Kappa < 0.75). Differences between all kits were statistically significant (P < 0.001). The reproducibility of RT-qPCR kits was determined using a coefficients of variation (CV) between 0.95% and 2.57%, indicating good reproducibility. CONCLUSIONS: This is the first comparative study to evaluate CPA and RT-qPCR kits' specificity and sensitivity for SARS-CoV-2 detection, and could serve as a reference for clinical laboratories, thus informing testing protocols amid the rapidly progressing COVID-19 pandemic.