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      Time series forecasting of new cases and new deaths rate for COVID-19 using deep learning methods

      research-article
      a , b , c , d , e , f , g , c , c , h , * , i , h , j , k , *
      Results in Physics
      The Authors. Published by Elsevier B.V.
      ANFIS, Adaptive Network-based Fuzzy Inference System, ANN, Artificial Neural Network, AU, Australia, Bi-GRU, Bidirectional Gated Recurrent Unit, Bi-Conv-LSTM, Bidirectional Convolutional Long Short Term Memory, Bi-LSTM, Bidirectional Long Short-Term Memory, Conv-LSTM, Convolutional Long Short Term Memory, COVID-19, Coronavirus Disease 2019, DL, Deep Learning, DLSTM, Delayed Long Short-Term Memory, EMRO, Eastern Mediterranean Regional Office, ES, Exponential Smoothing, EV, Explained Variance, GRU, Gated Recurrent Unit, IR, Iran, Lasso, Least Absolute Shrinkage and Selection Operator, LR, Linear Regression, LSTM, Long Short-Term Memory, MAE, Mean Absolute Error, MAPE, Mean Absolute Percentage Error, MSE, Mean Square Error, MERS, Middle East Respiratory Syndrome, ML, Machine Learning, MLP-ICA, Multi-layered Perceptron-Imperialist Competitive Calculation, MSLE, Mean Squared Log Error, PRISMA, Preferred Reporting Items for Precise Surveys and Meta-Analyses, ReLU, Rectified Linear Unit, RMSE, Root Mean Square Error, RMSLE, Root Mean Squared Log Error, RNN, Repetitive Neural Network, SARS, Serious Intense Respiratory Disorder, SARS-COV, SARS coronavirus, SARS-COV-2, Serious Intense Respiratory Disorder Coronavirus 2, SVM, Support Vector Machine, VAE, Variational Auto Encoder, WHO, World Health Organization, WPRO, Western Pacific Regional Office, Long Short Term Memory (LSTM), Convolutional Long Short Term Memory (Conv-LSTM), Gated Recurrent Unit (GRU), Bidirectional, New Cases of COVID-19, New Deaths of COVID-19, COVID-19 Prediction, Deep learning, Machine learning

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          Abstract

          The first known case of Coronavirus disease 2019 (COVID-19) was identified in December 2019. It has spread worldwide, leading to an ongoing pandemic, imposed restrictions and costs to many countries. Predicting the number of new cases and deaths during this period can be a useful step in predicting the costs and facilities required in the future. The purpose of this study is to predict new cases and deaths rate one, three and seven-day ahead during the next 100 days. The motivation for predicting every n days (instead of just every day) is the investigation of the possibility of computational cost reduction and still achieving reasonable performance. Such a scenario may be encountered in real-time forecasting of time series. Six different deep learning methods are examined on the data adopted from the WHO website. Three methods are LSTM, Convolutional LSTM, and GRU. The bidirectional extension is then considered for each method to forecast the rate of new cases and new deaths in Australia and Iran countries.

          This study is novel as it carries out a comprehensive evaluation of the aforementioned three deep learning methods and their bidirectional extensions to perform prediction on COVID-19 new cases and new death rate time series. To the best of our knowledge, this is the first time that Bi-GRU and Bi-Conv-LSTM models are used for prediction on COVID-19 new cases and new deaths time series. The evaluation of the methods is presented in the form of graphs and Friedman statistical test. The results show that the bidirectional models have lower errors than other models. A several error evaluation metrics are presented to compare all models, and finally, the superiority of bidirectional methods is determined. This research could be useful for organisations working against COVID-19 and determining their long-term plans.

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          Most cited references33

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          A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster

          Summary Background An ongoing outbreak of pneumonia associated with a novel coronavirus was reported in Wuhan city, Hubei province, China. Affected patients were geographically linked with a local wet market as a potential source. No data on person-to-person or nosocomial transmission have been published to date. Methods In this study, we report the epidemiological, clinical, laboratory, radiological, and microbiological findings of five patients in a family cluster who presented with unexplained pneumonia after returning to Shenzhen, Guangdong province, China, after a visit to Wuhan, and an additional family member who did not travel to Wuhan. Phylogenetic analysis of genetic sequences from these patients were done. Findings From Jan 10, 2020, we enrolled a family of six patients who travelled to Wuhan from Shenzhen between Dec 29, 2019 and Jan 4, 2020. Of six family members who travelled to Wuhan, five were identified as infected with the novel coronavirus. Additionally, one family member, who did not travel to Wuhan, became infected with the virus after several days of contact with four of the family members. None of the family members had contacts with Wuhan markets or animals, although two had visited a Wuhan hospital. Five family members (aged 36–66 years) presented with fever, upper or lower respiratory tract symptoms, or diarrhoea, or a combination of these 3–6 days after exposure. They presented to our hospital (The University of Hong Kong-Shenzhen Hospital, Shenzhen) 6–10 days after symptom onset. They and one asymptomatic child (aged 10 years) had radiological ground-glass lung opacities. Older patients (aged >60 years) had more systemic symptoms, extensive radiological ground-glass lung changes, lymphopenia, thrombocytopenia, and increased C-reactive protein and lactate dehydrogenase levels. The nasopharyngeal or throat swabs of these six patients were negative for known respiratory microbes by point-of-care multiplex RT-PCR, but five patients (four adults and the child) were RT-PCR positive for genes encoding the internal RNA-dependent RNA polymerase and surface Spike protein of this novel coronavirus, which were confirmed by Sanger sequencing. Phylogenetic analysis of these five patients' RT-PCR amplicons and two full genomes by next-generation sequencing showed that this is a novel coronavirus, which is closest to the bat severe acute respiatory syndrome (SARS)-related coronaviruses found in Chinese horseshoe bats. Interpretation Our findings are consistent with person-to-person transmission of this novel coronavirus in hospital and family settings, and the reports of infected travellers in other geographical regions. Funding The Shaw Foundation Hong Kong, Michael Seak-Kan Tong, Respiratory Viral Research Foundation Limited, Hui Ming, Hui Hoy and Chow Sin Lan Charity Fund Limited, Marina Man-Wai Lee, the Hong Kong Hainan Commercial Association South China Microbiology Research Fund, Sanming Project of Medicine (Shenzhen), and High Level-Hospital Program (Guangdong Health Commission).
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            Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial

            Background Chloroquine and hydroxychloroquine have been found to be efficient on SARS-CoV-2, and reported to be efficient in Chinese COV-19 patients. We evaluate the role of hydroxychloroquine on respiratory viral loads. Patients and methods French Confirmed COVID-19 patients were included in a single arm protocol from early March to March 16th, to receive 600mg of hydroxychloroquine daily and their viral load in nasopharyngeal swabs was tested daily in a hospital setting. Depending on their clinical presentation, azithromycin was added to the treatment. Untreated patients from another center and cases refusing the protocol were included as negative controls. Presence and absence of virus at Day6-post inclusion was considered the end point. Results Six patients were asymptomatic, 22 had upper respiratory tract infection symptoms and eight had lower respiratory tract infection symptoms. Twenty cases were treated in this study and showed a significant reduction of the viral carriage at D6-post inclusion compared to controls, and much lower average carrying duration than reported of untreated patients in the literature. Azithromycin added to hydroxychloroquine was significantly more efficient for virus elimination. Conclusion Despite its small sample size our survey shows that hydroxychloroquine treatment is significantly associated with viral load reduction/disappearance in COVID-19 patients and its effect is reinforced by azithromycin.
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              Transmission of 2019-nCoV Infection from an Asymptomatic Contact in Germany

              To the Editor: The novel coronavirus (2019-nCoV) from Wuhan is currently causing concern in the medical community as the virus is spreading around the world. 1 Since identification of the virus in late December 2019, the number of cases from China that have been imported into other countries is on the rise, and the epidemiologic picture is changing on a daily basis. We are reporting a case of 2019-nCoV infection acquired outside Asia in which transmission appears to have occurred during the incubation period in the index patient. A 33-year-old otherwise healthy German businessman (Patient 1) became ill with a sore throat, chills, and myalgias on January 24, 2020. The following day, a fever of 39.1°C (102.4°F) developed, along with a productive cough. By the evening of the next day, he started feeling better and went back to work on January 27. Before the onset of symptoms, he had attended meetings with a Chinese business partner at his company near Munich on January 20 and 21. The business partner, a Shanghai resident, had visited Germany between January 19 and 22. During her stay, she had been well with no signs or symptoms of infection but had become ill on her flight back to China, where she tested positive for 2019-nCoV on January 26 (index patient in Figure 1) (see Supplementary Appendix, available at NEJM.org, for details on the timeline of symptom development leading to hospitalization). On January 27, she informed the company about her illness. Contact tracing was started, and the above-mentioned colleague was sent to the Division of Infectious Diseases and Tropical Medicine in Munich for further assessment. At presentation, he was afebrile and well. He reported no previous or chronic illnesses and had no history of foreign travel within 14 days before the onset of symptoms. Two nasopharyngeal swabs and one sputum sample were obtained and were found to be positive for 2019-nCoV on quantitative reverse-transcriptase–polymerase-chain-reaction (qRT-PCR) assay. 2 Follow-up qRT-PCR assay revealed a high viral load of 108 copies per milliliter in his sputum during the following days, with the last available result on January 29. On January 28, three additional employees at the company tested positive for 2019-nCoV (Patients 2 through 4 in Figure 1). Of these patients, only Patient 2 had contact with the index patient; the other two patients had contact only with Patient 1. In accordance with the health authorities, all the patients with confirmed 2019-nCoV infection were admitted to a Munich infectious diseases unit for clinical monitoring and isolation. So far, none of the four confirmed patients show signs of severe clinical illness. This case of 2019-nCoV infection was diagnosed in Germany and transmitted outside Asia. However, it is notable that the infection appears to have been transmitted during the incubation period of the index patient, in whom the illness was brief and nonspecific. 3 The fact that asymptomatic persons are potential sources of 2019-nCoV infection may warrant a reassessment of transmission dynamics of the current outbreak. In this context, the detection of 2019-nCoV and a high sputum viral load in a convalescent patient (Patient 1) arouse concern about prolonged shedding of 2019-nCoV after recovery. Yet, the viability of 2019-nCoV detected on qRT-PCR in this patient remains to be proved by means of viral culture. Despite these concerns, all four patients who were seen in Munich have had mild cases and were hospitalized primarily for public health purposes. Since hospital capacities are limited — in particular, given the concurrent peak of the influenza season in the northern hemisphere — research is needed to determine whether such patients can be treated with appropriate guidance and oversight outside the hospital.
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                Author and article information

                Journal
                Results Phys
                Results Phys
                Results in Physics
                The Authors. Published by Elsevier B.V.
                2211-3797
                26 June 2021
                August 2021
                26 June 2021
                : 27
                : 104495
                Affiliations
                [a ]Department of Mathematics, Savitribai Phule Pune University, Pune 411007, India
                [b ]Department of Computer Engineering, School of Technical and Engineering, Shiraz Branch, Islamic Azad University, Shiraz, Iran
                [c ]Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Waurn Ponds, VIC 3217, Australia
                [d ]Computer Engineering Department, Ferdowsi University of Mashhad, Mashhad, Iran
                [e ]Faculty of Electrical and Computer Engineering, Biomedical Data Acquisition Lab, K. N. Toosi University of Technology, Tehran, Iran
                [f ]Department of Signal Theory, Networking and Communications, Universidad de Granada, Spain
                [g ]Department of Mathematics, Faculty of Science, University of Bojnord, Iran
                [h ]Sustainable Process Integration Laboratory - SPIL, NETME Centre, Faculty of Mechanical Engineering, Brno University of Technology - VUT Brno, Technická 2896/2, 616 69 Brno, Czech Republic
                [i ]Department of Management, Faculty of Business and Management, Brno University of Technology - VUT Brno, Kolejní 2906/4, 612 00 Brno, Czech Republic
                [j ]John von Neumann Faculty of Informatics, Obuda University, 1034 Budapest, Hungary
                [k ]School of Economics and Business, Norwegian University of Life Sciences, 1430 Ås, Norway
                Author notes
                [* ]Corresponding authors at: Sustainable Process Integration Laboratory - SPIL, NETME Centre, Faculty of Mechanical Engineering, Brno University of Technology - VUT Brno, Technická 2896/2, 616 69 Brno, Czech Republic (A.G. Chofreh) and John von Neumann Faculty of Informatics, Obuda University, 1034 Budapest, Hungary (A. Mosavi). (A. Mosavi).
                Article
                S2211-3797(21)00606-9 104495
                10.1016/j.rinp.2021.104495
                8233414
                34221854
                7455f35a-35b7-49fe-bf1f-5f9e57ac2246
                © 2021 The Authors

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                : 22 March 2021
                : 19 June 2021
                : 22 June 2021
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                anfis, adaptive network-based fuzzy inference system,ann, artificial neural network,au, australia,bi-gru, bidirectional gated recurrent unit,bi-conv-lstm, bidirectional convolutional long short term memory,bi-lstm, bidirectional long short-term memory,conv-lstm, convolutional long short term memory,covid-19, coronavirus disease 2019,dl, deep learning,dlstm, delayed long short-term memory,emro, eastern mediterranean regional office,es, exponential smoothing,ev, explained variance,gru, gated recurrent unit,ir, iran,lasso, least absolute shrinkage and selection operator,lr, linear regression,lstm, long short-term memory,mae, mean absolute error,mape, mean absolute percentage error,mse, mean square error,mers, middle east respiratory syndrome,ml, machine learning,mlp-ica, multi-layered perceptron-imperialist competitive calculation,msle, mean squared log error,prisma, preferred reporting items for precise surveys and meta-analyses,relu, rectified linear unit,rmse, root mean square error,rmsle, root mean squared log error,rnn, repetitive neural network,sars, serious intense respiratory disorder,sars-cov, sars coronavirus,sars-cov-2, serious intense respiratory disorder coronavirus 2,svm, support vector machine,vae, variational auto encoder,who, world health organization,wpro, western pacific regional office,long short term memory (lstm),convolutional long short term memory (conv-lstm),gated recurrent unit (gru),bidirectional,new cases of covid-19,new deaths of covid-19,covid-19 prediction,deep learning,machine learning
                anfis, adaptive network-based fuzzy inference system, ann, artificial neural network, au, australia, bi-gru, bidirectional gated recurrent unit, bi-conv-lstm, bidirectional convolutional long short term memory, bi-lstm, bidirectional long short-term memory, conv-lstm, convolutional long short term memory, covid-19, coronavirus disease 2019, dl, deep learning, dlstm, delayed long short-term memory, emro, eastern mediterranean regional office, es, exponential smoothing, ev, explained variance, gru, gated recurrent unit, ir, iran, lasso, least absolute shrinkage and selection operator, lr, linear regression, lstm, long short-term memory, mae, mean absolute error, mape, mean absolute percentage error, mse, mean square error, mers, middle east respiratory syndrome, ml, machine learning, mlp-ica, multi-layered perceptron-imperialist competitive calculation, msle, mean squared log error, prisma, preferred reporting items for precise surveys and meta-analyses, relu, rectified linear unit, rmse, root mean square error, rmsle, root mean squared log error, rnn, repetitive neural network, sars, serious intense respiratory disorder, sars-cov, sars coronavirus, sars-cov-2, serious intense respiratory disorder coronavirus 2, svm, support vector machine, vae, variational auto encoder, who, world health organization, wpro, western pacific regional office, long short term memory (lstm), convolutional long short term memory (conv-lstm), gated recurrent unit (gru), bidirectional, new cases of covid-19, new deaths of covid-19, covid-19 prediction, deep learning, machine learning

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