69
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Deep Learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) With CT Images

      brief-report

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          A novel coronavirus (COVID-19) recently emerged as an acute respiratory syndrome, and has caused a pneumonia outbreak world-widely. As the COVID-19 continues to spread rapidly across the world, computed tomography (CT) has become essentially important for fast diagnoses. Thus, it is urgent to develop an accurate computer-aided method to assist clinicians to identify COVID-19-infected patients by CT images. Here, we have collected chest CT scans of 88 patients diagnosed with COVID-19 from hospitals of two provinces in China, 100 patients infected with bacteria pneumonia, and 86 healthy persons for comparison and modeling. Based on the data, a deep learning-based CT diagnosis system was developed to identify patients with COVID-19. The experimental results showed that our model could accurately discriminate the COVID-19 patients from the bacteria pneumonia patients with an AUC of 0.95, recall (sensitivity) of 0.96, and precision of 0.79. When integrating three types of CT images, our model achieved a recall of 0.93 with precision of 0.86 for discriminating COVID-19 patients from others. Moreover, our model could extract main lesion features, especially the ground-glass opacity (GGO), which are visually helpful for assisted diagnoses by doctors. An online server is available for online diagnoses with CT images by our server ( http://biomed.nscc-gz.cn/model.php). Source codes and datasets are available at our GitHub ( https://github.com/SY575/COVID19-CT).

          Related collections

          Most cited references24

          • Record: found
          • Abstract: found
          • Article: not found

          Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

          Summary Background A recent cluster of pneumonia cases in Wuhan, China, was caused by a novel betacoronavirus, the 2019 novel coronavirus (2019-nCoV). We report the epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes of these patients. Methods All patients with suspected 2019-nCoV were admitted to a designated hospital in Wuhan. We prospectively collected and analysed data on patients with laboratory-confirmed 2019-nCoV infection by real-time RT-PCR and next-generation sequencing. Data were obtained with standardised data collection forms shared by WHO and the International Severe Acute Respiratory and Emerging Infection Consortium from electronic medical records. Researchers also directly communicated with patients or their families to ascertain epidemiological and symptom data. Outcomes were also compared between patients who had been admitted to the intensive care unit (ICU) and those who had not. Findings By Jan 2, 2020, 41 admitted hospital patients had been identified as having laboratory-confirmed 2019-nCoV infection. Most of the infected patients were men (30 [73%] of 41); less than half had underlying diseases (13 [32%]), including diabetes (eight [20%]), hypertension (six [15%]), and cardiovascular disease (six [15%]). Median age was 49·0 years (IQR 41·0–58·0). 27 (66%) of 41 patients had been exposed to Huanan seafood market. One family cluster was found. Common symptoms at onset of illness were fever (40 [98%] of 41 patients), cough (31 [76%]), and myalgia or fatigue (18 [44%]); less common symptoms were sputum production (11 [28%] of 39), headache (three [8%] of 38), haemoptysis (two [5%] of 39), and diarrhoea (one [3%] of 38). Dyspnoea developed in 22 (55%) of 40 patients (median time from illness onset to dyspnoea 8·0 days [IQR 5·0–13·0]). 26 (63%) of 41 patients had lymphopenia. All 41 patients had pneumonia with abnormal findings on chest CT. Complications included acute respiratory distress syndrome (12 [29%]), RNAaemia (six [15%]), acute cardiac injury (five [12%]) and secondary infection (four [10%]). 13 (32%) patients were admitted to an ICU and six (15%) died. Compared with non-ICU patients, ICU patients had higher plasma levels of IL2, IL7, IL10, GSCF, IP10, MCP1, MIP1A, and TNFα. Interpretation The 2019-nCoV infection caused clusters of severe respiratory illness similar to severe acute respiratory syndrome coronavirus and was associated with ICU admission and high mortality. Major gaps in our knowledge of the origin, epidemiology, duration of human transmission, and clinical spectrum of disease need fulfilment by future studies. Funding Ministry of Science and Technology, Chinese Academy of Medical Sciences, National Natural Science Foundation of China, and Beijing Municipal Science and Technology Commission.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia

            Abstract Background The initial cases of novel coronavirus (2019-nCoV)–infected pneumonia (NCIP) occurred in Wuhan, Hubei Province, China, in December 2019 and January 2020. We analyzed data on the first 425 confirmed cases in Wuhan to determine the epidemiologic characteristics of NCIP. Methods We collected information on demographic characteristics, exposure history, and illness timelines of laboratory-confirmed cases of NCIP that had been reported by January 22, 2020. We described characteristics of the cases and estimated the key epidemiologic time-delay distributions. In the early period of exponential growth, we estimated the epidemic doubling time and the basic reproductive number. Results Among the first 425 patients with confirmed NCIP, the median age was 59 years and 56% were male. The majority of cases (55%) with onset before January 1, 2020, were linked to the Huanan Seafood Wholesale Market, as compared with 8.6% of the subsequent cases. The mean incubation period was 5.2 days (95% confidence interval [CI], 4.1 to 7.0), with the 95th percentile of the distribution at 12.5 days. In its early stages, the epidemic doubled in size every 7.4 days. With a mean serial interval of 7.5 days (95% CI, 5.3 to 19), the basic reproductive number was estimated to be 2.2 (95% CI, 1.4 to 3.9). Conclusions On the basis of this information, there is evidence that human-to-human transmission has occurred among close contacts since the middle of December 2019. Considerable efforts to reduce transmission will be required to control outbreaks if similar dynamics apply elsewhere. Measures to prevent or reduce transmission should be implemented in populations at risk. (Funded by the Ministry of Science and Technology of China and others.)
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

              Summary Background In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed. Methods We did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus. Findings The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues. Interpretation 2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensin-converting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent investigation. Funding National Key Research and Development Program of China, National Major Project for Control and Prevention of Infectious Disease in China, Chinese Academy of Sciences, Shandong First Medical University.
                Bookmark

                Author and article information

                Contributors
                Journal
                IEEE/ACM Trans Comput Biol Bioinform
                IEEE/ACM Trans Comput Biol Bioinform
                0065500
                TCBB
                ITCBCY
                Ieee/Acm Transactions on Computational Biology and Bioinformatics
                IEEE
                1545-5963
                1557-9964
                01 November 2021
                11 March 2021
                : 18
                : 6
                : 2775-2780
                Affiliations
                [1] divisionNational Supercomputer Center in Guangzhou, institutionSun Yat-sen University; Guangzhou 510006 China
                [2] divisionSchool of Systems Sciences and Engineering, institutionSun Yat-sen University; Guangzhou 510006 China
                [3] divisionNational Supercomputer Center in Guangzhou, institutionSun Yat-sen University; Guangzhou 510006 China
                [4] divisionDepartment of Radiology, institutionRenmin Hospital of Wuhan University; Wuhan 430060 China
                [5] divisionDepartment of Radiology, Sun Yat-Sen Memorial Hospital, institutionSun Yat-Sen University; Guangzhou 510530 China
                [6] divisionDepartment of Radiology, institutionThe Third Affiliated Hospital of Sun Yat-Sen University; Guangzhou 510220 China
                [7] divisionSchool of Data and Computer Science, institutionSun Yat-sen University; Guangzhou 510006 China
                [8] divisionNational Supercomputer Center in Guangzhou, institutionSun Yat-sen University; Guangzhou 510006 China
                [9] divisionSchool of Data and Computer Science, institutionSun Yat-sen University; Guangzhou 510006 China
                Article
                10.1109/TCBB.2021.3065361
                8851430
                33705321
                f4862b11-4dd6-4835-8a5b-23672403ec3b
                Copyright @ 2021

                This article is free to access and download, along with rights for full text and data mining, re-use and analysis.

                History
                : 17 April 2020
                : 10 February 2021
                : 27 February 2021
                : 08 December 2021
                Page count
                Figures: 5, Tables: 2, References: 28, Pages: 6
                Funding
                Funded by: institutionNational Key Research and Development Program of China, fundref 10.13039/501100012166;
                Award ID: 2018YFC1315405
                Funded by: institutionNational Natural Science Foundation of China, fundref 10.13039/501100001809;
                Award ID: U1611261
                Award ID: 61772566
                Award ID: 81801132
                Award ID: 81871332
                Funded by: institutionGuangdong Frontier and Key Tech Innovation Program;
                Award ID: 2018B010109006
                Award ID: 2019B020228001
                Funded by: institutionNatural Science Foundation of Guangdong Province, fundref 10.13039/501100003453;
                Award ID: 2019A1515012207
                Funded by: institutionIntroducing Innovative and Entrepreneurial Teams;
                Award ID: 2016ZT06D211
                The work was supported in part by the National Key R&D Program of China under Grant 2018YFC1315405, the National Natural Science Foundation of China under Grants U1611261, 61772566, 81801132 and 81871332, Guangdong Frontier and Key Tech Innovation Program under Grants 2018B010109006 and 2019B020228001, the Natural Science Foundation of Guangdong, China under Grant 2019A1515012207, and Introducing Innovative and Entrepreneurial Teams under Grant 2016ZT06D211.
                Categories
                Article

                covid-19,deep learning,pneumonia diagnosis,weakly supervised learning

                Comments

                Comment on this article