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Covid-19 Diagnosis system
Background The coronavirus belongs to a family of viruses that may cause various symptoms such as pneumonia, fever, breathing difficulty, and lung infection [1]. These viruses are common in animals worldwide, but very few cases have been known to affect humans. The World Health Organization (WHO) used the term 2019 novel coronavirus to refer to a coronavirus that affected the lower respiratory tract of patients with pneumonia in Wuhan, China on 29 December 2019 [2,3,4]. The WHO announced that the official name of the 2019 novel coronavirus is coronavirus disease (COVID-19) [4]. And the current reference name for the virus is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It was reported that a cluster of patients with pneumonia of unknown cause was linked to a local Huanan South China Seafood Market in Wuhan, Hubei Province, China in December 2019 [5].
In response to the outbreak, the Chinese Center for Disease Control and Prevention (China CDC) dispatched a rapid response team to accompany health authorities of Hubei province and Wuhan city to conduct epidemiological and etiological investigations. The WHO confirmed that the outbreak of the coronavirus epidemic was associated with the Huanan South China Seafood Marketplace, but no specific animal association was identified [6]. Scientists immediately started to research the source of the new coronavirus, and the first genome of COVID-19 was published by the research team led by Prof. Yong-Zhen Zhang, on 10 January 2020 [7]. Within 1 month, this virus spread quickly throughout China during the Chinese New Year – a period when there is a high level of human mobility among Chinese people. Although it is still too early to predict susceptible populations, early patterns have shown a trend similar to Severe Acute Respiratory Syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses. Susceptibility seems to be associated with age, biological sex, and other health conditions [8]. COVID-19 has now been declared as a Public Health Emergency of International Concern by the WHO [9].
Given the spread of the new coronavirus and its impacts on human health, the research community has responded rapidly to the new virus and many preliminary research articles have already been published about this epidemic (Additional file 1). We conducted a scoping review to summarize and critically analyze all the published scientific articles regarding the new coronavirus in January 2020. This review aims to provide the evidence of early findings on the epidemiology, causes, clinical diagnosis, as well as prevention and control of COVID-19 in relation to time, location, and source of publication. This review can provide meaningful information for future research related to this topic and may support government decision-making on strategies to handle this public health emergency at the community, national, and international levels.
Methods Study design A scoping review was conducted following the methodological framework suggested by Arksey and O’Malley [10]. The following five steps were followed to conduct this scoping review: a) identifying a clear research objective and search strategies, b) identifying relevant research articles, c) selection of research articles, d) extraction and charting of data, and e) summarizing, discussing, analyzing, and reporting the results.
Literature search strategies Literature for this review was identified by searching the following online databases: bioRxiv, medRxiv, ChemRxiv, Google scholar, PubMed, as well as CNKI and WanFang Data (the two primary databases for biomedical research in mainland China). These online databases contain archives of most English and Chinese biomedical journals. In addition, some white papers published online by the National Health Commission of the People’s Republic of China, Chinese Center for Disease Prevention and Control, and the WHO were included in the analysis. We searched scientific publications from 1 January to 31 January 2020. The search terms were ‘nCoV’, ‘2019 novel coronavirus’, ‘2019-nCoV’, ‘novel coronavirus’, ‘Pneumonia’, ‘新型冠状病毒’ (Chinese), ‘新型肺炎’ (Chinese), and ‘新冠病毒’ (Chinese). We included all the relevant scientific publications written in English or Chinese in the review. Non-scientific commentary, reports, and news articles were excluded from the analysis.
Identification and selection of relevant studies Two researchers (YW and SPA) independently searched through the literature. The two sets of literature were then compared. Disagreements on the inclusion or exclusion of literature were resolved through discussion or, if necessary, by including a third researcher (HZ) to make the final decision. Duplicate articles were eliminated. Eventually, 65 unique academic publications were included in this analysis (Additional file 1). Figure 1 presents a Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) flow diagram showing the process of searching and selecting the research articles [11].
Fig. 1 figure1 PRISMA flow diagram for the scoping review process
Full size image Data extraction from the included studies After the articles were selected, data were extracted and recorded in an excel spreadsheet. The extracted data were date of publication, language of publication, title of article, name of journal, author’s country and affiliation, study design, targets of study, sample size, study setting, data collection instrument, research domain, and key findings.
Summarizing the findings Based on the main research objectives, articles were classified into one of the following four research domains: epidemiology, causes, clinical manifestation and diagnosis, or prevention and control. ‘Epidemiology’ includes studies on the epidemic distribution (when, where, who); ‘causes’ includes studies on virology, pathogenesis, and transmission patterns; ‘clinical manifestation and diagnosis’ includes studies on the clinical features (signs and symptoms) and diagnosis; and ‘prevention and control’ includes studies on prevention, control, and treatment measures.
Authors’ affiliations were used to categorize the type of research collaboration. A publication was considered as deriving from ‘inside China’ when all affiliations of the authors were from China; a publication was considered as deriving from ‘outside China’ when all affiliations were outside China; a publication was considered as deriving from ‘international collaboration’ when at least one affiliation was from China and at least one was from outside China. The research domains, publishing dates, journal language, authors’ affiliations, as well as methodological characteristics were analyzed respectively. All findings and statements regarding the outbreak in this review are based on published information as listed in the references.
Results and discussion Characteristics of published studies Among the 65 research articles included in the analysis, more than 31 are on preprint servers, and 34 are published in peer-reviewed journals, including The Lancet and The New England Journal of Medicine. Most of the publications (n = 58, 89.2%) are in English and few (n = 7, 10.8%) are in Chinese. Around 75.9% of English language publications focus on epidemiology and causes, while 85.7% of Chinese papers focus on prevention and control (Table 1).
Table 1 Breakdown of research domains by language in January 2020 Full size table As shown in Fig. 2, academic publications are distributed across the following research domains: epidemiology, causes, clinical manifestation and diagnosis, and prevention and control. The largest portion of the papers (n = 25, 38.5%) are related to causes, followed by papers on epidemiology (n = 19, 29.2%), while 18.5% examined prevention and control and 13.8% reported clinical manifestations and diagnosis. Initially, there were more research articles focused on causes of the outbreak, yet studies on prevention and control gradually increased over time (Fig. 3). The majority of the articles (n = 44, 67.7%) were published by Chinese scholars whereas 29.2% (n = 19) articles were from scholars outside of China. A small number (n = 2, 3.1%) were based on international collaborative research by scholars from different countries (Table 2).
Fig. 2 figure2 Research domains of published research articles
Full size image Fig. 3 figure3 Publication dates of research articles
Full size image Table 2 Breakdown of research domains by collaboration type in January 2020 Full size table We also analyzed the methodological characteristics of the publications in the final sample. The majority of the articles are based on mathematical modeling (44.6%) and cross-sectional study designs (18.5%). Around half of the studies include targeted populations (patients, general populations, and healthcare workers) (49.2%) in their analysis, followed by studies that attempt to identify the species of the virus (virus structure, gene sequence) (36.9%). Among the 32 articles with population as the target of study, 34.4% had a sample size of less than 10, 31.3% were conducted in a hospital setting, and 50% used secondary data. Quality control activities for data collection were mentioned in 56.3% of the population studies (Table 3).
Table 3 Methodological characteristics of COVID-19 research articles in January 2020 Full size table Research domains Epidemiology On 29 December 2019, the first four cases of an acute respiratory syndrome of unknown etiology were reported in Wuhan City, Hubei Province, China among people linked to a local seafood market (“wet market”) [2]. Research is underway to understand more about transmissibility, severity, and other features associated with COVID-19 [3]. It appears that most of the early cases had some sort of contact history with the original seafood market [2, 12,13,14]. Soon, a secondary source of infection was found to be human-to-human transmission via close contact. There was an increase of infected people with no history of exposure to wildlife or visiting Wuhan, and multiple cases of infection were detected among medical professionals [2, 14,15,16,17]. It became clear that the COVID-19 infection occurs through exposure to the virus, and both the immunosuppressed and normal population appear susceptible. Some studies have reported an age distribution of adult patients between 25 and 89 years old. Most adult patients were between 35 and 55 years old [14], and there were fewer identified cases among children and infants [14, 18]. A study on early transmission dynamics of the virus reported the median age of patients to be 59 years, ranging from 15 to 89 years, with the majority (59%) being male [2]. It was suggested that the population most at risk may be people with poor immune function such as older people and those with renal and hepatic dysfunction [2].
The COVID-19 has been found to have higher levels of transmissibility and pandemic risk than the SARS-CoV, as the effective reproductive number (R) of COVID-19 (2.9) is estimated to be higher than the reported effective reproduction number (R) of SARS (1.77) at this early stage [15]. Different studies of COVID-19 have estimated the basic reproduction (R0) range to be from 2.6 to 4.71 (Table 4). The average incubation duration of COVID-19 was estimated to be 4.8 ± 2.6, ranging from 2 to 11 days [15] and 5.2 days (95% confidence interval, 4.1 to 7) [2]. The latest guidelines from Chinese health authorities stated an average incubation duration of 7 days, ranging from 2 to 14 days [23]. Table 4 summarizes the findings on important indicators from these epidemiological studies.
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