covis_testdata.json

{
  "context": {
    "id": "covid19",
    "params": {
      "q": "covid19",
      "service": "gsheets",
      "vis_id": "covid19",
      "vis_type": "overview"
    },
    "query": "covid19",
    "service": "gsheets",
    "timestamp": "Tue, 07 Apr 2020 14:10:25 GMT"
  },
  "data": [
    {
      "area": "Vaccines",
      "area_uri": 0,
      "authors": "Du, Lanying; He, Yuxian; Zhou, Yusen; Liu, Shuwen; Zheng, Bo-Jian; Jiang, Shibo",
      "cluster_labels": "2019 Wuhan novel, 2019-ncov indicate evolutionary, Conserved functional regions",
      "comments": "The vaccination efforts are focused on the major surface protein of coronavirus called spike protein",
      "id": "https://doi.org/10.1038/nrmicro2090",
      "lang_detected": "english",
      "link": "https://www.nature.com/articles/nrmicro2090.pdf",
      "oa_state": 3,
      "paper_abstract": "Severe acute respiratory syndrome (SARS) is a newly emerging infectious disease caused by a novel coronavirus, SARS-coronavirus (SARS-CoV). The SARS-CoV spike (S) protein is composed of two subunits; the S1 subunit contains a receptor-binding domain that engages with the host cell receptor angiotensin-converting enzyme 2 and the S2 subunit mediates fusion between the viral and host cell membranes. The S protein plays key parts in the induction of neutralizing-antibody and T-cell responses, as well as protective immunity, during infection with SARS-CoV. In this Review, we highlight recent advances in the development of vaccines and therapeutics based on the S protein.",
      "published_in": "Nature Reviews Microbiology volume 7, pages226–236",
      "readers": 0,
      "relevance": 2,
      "resulttype": "Review",
      "subject": "Spike protein, vaccines",
      "tags": "Peer-reviewed",
      "title": "The spike protein of SARS-CoV — a target for vaccine and therapeutic development",
      "url": "https://www.nature.com/articles/nrmicro2090.pdf",
      "x": "-0.397598278782077",
      "y": "0.150118395823645",
      "year": "2020-02-09"
    },
    {
      "area": "Viral biology",
      "area_uri": 1,
      "authors": "Cui, Hongzhu; Gao, Ziyang; Liu, Ming; Lu, Senbao; Mo, Sun; Mkandawire, Winnie; Narykov, Oleksandr; Srinivasan, Suhas; Korkin, Dmitry",
      "cluster_labels": "2019 Wuhan novel, 2019-ncov indicate evolutionary, Conserved functional regions",
      "comments": "",
      "id": "https://doi.org/10.1101/2020.02.10.942136 ",
      "lang_detected": "english",
      "link": "https://www.biorxiv.org/content/10.1101/2020.02.10.942136v1.full.pdf",
      "oa_state": 1,
      "paper_abstract": "During its first month, the recently emerged 2019 Wuhan novel coronavirus (2019-nCoV) has already infected many thousands of people in mainland China and worldwide and took hundreds of lives. However, the swiftly spreading virus also caused an unprecedentedly rapid response from the research community facing the unknown health challenge of potentially enormous proportions. Unfortunately, the experimental research to understand the molecular mechanisms behind the viral infection and to design a vaccine or antivirals is costly and takes months to develop. To expedite the advancement of our knowledge we leverage the data about the related coronaviruses that is readily available in public databases, and integrate these data into a single computational pipeline. As a result, we provide a comprehensive structural genomics and interactomics road-maps of 2019-nCoV and use these information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community at http://korkinlab.org/wuhan",
      "published_in": "bioRxiv",
      "readers": 0,
      "relevance": 3,
      "resulttype": "Preprint",
      "subject": "Viral proteins, structural, genomic, computational modeling",
      "tags": "reproducible",
      "title": "Structural genomics and interactomics of 2019 Wuhan novel coronavirus, 2019-nCoV, indicate evolutionary conserved functional regions of viral proteins",
      "url": "https://www.biorxiv.org/content/10.1101/2020.02.10.942136v1.full.pdf",
      "x": "-0.211850740206885",
      "y": "-0.0301770174302581",
      "year": "2020-02-14"
    },
    {
      "area": "Host biology and clinical findings",
      "area_uri": 2,
      "authors": "Goyal, Girija",
      "cluster_labels": "2015 South Korea, 2019 coronavirus, Coronavirus 2019-ncov SARSCov2",
      "comments": "Compilation of modeling and in vitro studies",
      "id": "https://refigure.org/collections/item/ecd1dab0-56a5-11ea-8c54-9323bc73fc6b/",
      "lang_detected": "english",
      "link": "N/A",
      "oa_state": 3,
      "paper_abstract": "Due to the high number of preprints being submitted on coronavirus, concerns have been raised about whether these findings are truly actionable.",
      "published_in": "ReFigure",
      "readers": 0,
      "relevance": 5,
      "resulttype": "ReFigure",
      "subject": "ileum, oral, gastrointestinal, receptor, ACE2, gene expression",
      "tags": "Collection, reproducible",
      "title": "Gastrointestinal system as a route of infection and transmission of 2019 coronavirus",
      "url": "N/A",
      "x": "-0.129621121125355",
      "y": "-0.287409553561853",
      "year": "2020-02-23"
    },
    {
      "area": "Therapeutics",
      "area_uri": 3,
      "authors": "Zhou, Yadi; Hou, Yuan; Shen, Jiayu; Huang, Yin; Martin, William; Cheng, Feixiong",
      "cluster_labels": "2015 South Korea, 2019 coronavirus, Coronavirus 2019-ncov SARSCov2",
      "comments": "A thoughful study identifying 16 drug combinations",
      "id": "https://doi.org/10.1038/s41421-020-0153-3",
      "lang_detected": "english",
      "link": "https://www.nature.com/articles/s41421-020-0153-3.pdf?origin=ppub",
      "oa_state": 1,
      "paper_abstract": "Human coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV) and 2019 novel coronavirus (2019-nCoV, also known as SARS-CoV-2), lead global epidemics with high morbidity and mortality. However, there are currently no effective drugs targeting 2019-nCoV/SARS-CoV-2. Drug repurposing, representing as an effective drug discovery strategy from existing drugs, could shorten the time and reduce the cost compared to de novo drug discovery. In this study, we present an integrative, antiviral drug repurposing methodology implementing a systems pharmacology-based network medicine platform, quantifying the interplay between the HCoV–host interactome and drug targets in the human protein–protein interaction network. Phylogenetic analyses of 15 HCoV whole genomes reveal that 2019-nCoV/SARS-CoV-2 shares the highest nucleotide sequence identity with SARS-CoV (79.7%). Specifically, the envelope and nucleocapsid proteins of 2019-nCoV/SARS-CoV-2 are two evolutionarily conserved regions, having the sequence identities of 96% and 89.6%, respectively, compared to SARS-CoV. Using network proximity analyses of drug targets and HCoV–host interactions in the human interactome, we prioritize 16 potential anti-HCoV repurposable drugs (e.g., melatonin, mercaptopurine, and sirolimus) that are further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. We further identify three potential drug combinations (e.g., sirolimus plus dactinomycin, mercaptopurine plus melatonin, and toremifene plus emodin) c aptured by the “Complementary Exposure” pattern: the targets of the drugs both hit the HCoV–host subnetwork, but target separate neighborhoods in the human interactome network. In summary, this study offers powerful network-based methodologies for rapid identification of candidate repurposable drugs and potential drug combinations targeting 2019-nCoV/SARS-CoV-2.",
      "published_in": "Cell Discovery",
      "readers": 0,
      "relevance": 6,
      "resulttype": "Journal Article",
      "subject": "Drug repurposing, computational modeling and prediction",
      "tags": "Peer-reviewed",
      "title": "Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2",
      "url": "https://www.nature.com/articles/s41421-020-0153-3.pdf?origin=ppub",
      "x": "-0.377616672787154",
      "y": "-0.227515104995169",
      "year": "2020-03-16"
    },
    {
      "area": "Epidemiology",
      "area_uri": 4,
      "authors": "Bwire, George M.; Paulo, Linda S.",
      "cluster_labels": "2 SARSCov2 epidemic, 2019-ncov outbreak originating, 21st century GIS",
      "comments": "",
      "id": "https://doi.org/10.1186/s41182-020-00201-2",
      "lang_detected": "english",
      "link": "https://tropmedhealth.biomedcentral.com/track/pdf/10.1186/s41182-020-00201-2",
      "oa_state": 1,
      "paper_abstract": "On Thursday, 30 January 2020, World Health Organization declared Coronavirus disease-2019 (COVID-2019) a Public Health Emergency of International Concern. Since its identification in late December 2019 in Wuhan, Hubei Province, People’s Republic of China, the number of cases imported into other countries is increasing, and the epidemiological map is changing rapidly. On the other hand, body temperature screening (fever) is the major test performed at points of entry, i.e., airports, in the returning travelers in most of the countries with limited resources. However, the recent report on asymptomatic contact transmission of COVID-19 and travelers who passed the symptoms-based screening and tested positive for COVID-19 using reverse transcription polymerase chain reaction (RT-PCR) challenges this approach as body temperature screening may miss travelers incubating the disease or travelers concealing fever during travel. On this note, travel restrictions to and from high risk areas and/or 14 days quarantine of travelers coming from high risk areas are recommended to prevent possible importation of COVID-19. Currently, RT-PCR is a reliable test in detecting both symptomatic and asymptomatic COVID-19.",
      "published_in": "Tropical Medicine and Health",
      "readers": 0,
      "relevance": 7,
      "resulttype": "Journal Article",
      "subject": "Screening, fever",
      "tags": "Perspective",
      "title": "Coronavirus disease-2019: is fever an adequate screening for the returning travelers?",
      "url": "https://tropmedhealth.biomedcentral.com/track/pdf/10.1186/s41182-020-00201-2",
      "x": "0.159372266922843",
      "y": "-0.343667508195378",
      "year": "2020-03-09"
    },
    {
      "area": "Epidemiology",
      "area_uri": 4,
      "authors": "Kamel Boulos, Maged N.; Geraghty, Estella M.",
      "cluster_labels": "2 SARSCov2 epidemic, 2019-ncov outbreak originating, 21st century GIS",
      "comments": "",
      "id": "https://doi.org/10.1186/s12942-020-00202-8",
      "lang_detected": "english",
      "link": "https://ij-healthgeographics.biomedcentral.com/track/pdf/10.1186/s12942-020-00202-8",
      "oa_state": 1,
      "paper_abstract": "In December 2019, a new virus (initially called ‘Novel Coronavirus 2019-nCoV’ and later renamed to SARS-CoV-2) causing severe acute respiratory syndrome (coronavirus disease COVID-19) emerged in Wuhan, Hubei Province, China, and rapidly spread to other parts of China and other countries around the world, despite China’s massive efforts to contain the disease within Hubei. As with the original SARS-CoV epidemic of 2002/2003 and with seasonal influenza, geographic information systems and methods, including, among other application possibilities, online real-or near-real-time mapping of disease cases and of social media reactions to disease spread, predictive risk mapping using population travel data, and tracing and mapping super-spreader trajectories and contacts across space and time, are proving indispensable for timely and effective epidemic monitoring and response. This paper offers pointers to, and describes, a range of practical online/mobile GIS and mapping dashboards and applications for tracking the 2019/2020 coronavirus epidemic and associated events as they unfold around the world. Some of these dashboards and applications are receiving data updates in near-real-time (at the time of writing), and one of them is meant for individual users (in China) to check if the app user has had any close contact with a person confirmed or suspected to have been infected with SARS-CoV-2 in the recent past. We also discuss additional ways GIS can support the fight against infectious disease outbreaks and epidemics.",
      "published_in": "International Journal of Health Geographics",
      "readers": 0,
      "relevance": 8,
      "resulttype": "Review",
      "subject": "Tracking technologies, GIS, geographic",
      "tags": "Peer-reviewed",
      "title": "Geographical tracking and mapping of coronavirus disease COVID-19/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic and associated events around the world: how 21st century GIS technologies are supporting the global fight against outbreaks and epidemics",
      "url": "https://ij-healthgeographics.biomedcentral.com/track/pdf/10.1186/s12942-020-00202-8",
      "x": "0.0083644529591441",
      "y": "-0.166922967126114",
      "year": "2020-03-11"
    },
    {
      "area": "Host biology and clinical findings",
      "area_uri": 2,
      "authors": "Shi, Yu; Yu, Xia; Zhao, Hong; Wang, Hao; Zhao, Ruihong; Sheng, Jifang",
      "cluster_labels": "15-year follow-up, 2019 novel coronavirus, 487 cases outside",
      "comments": "A large number of patients was studied in this report",
      "id": "https://doi.org/10.1186/s13054-020-2833-7",
      "lang_detected": "english",
      "link": "https://ccforum.biomedcentral.com/track/pdf/10.1186/s13054-020-2833-7",
      "oa_state": 1,
      "paper_abstract": "N/A",
      "published_in": "Critical Care",
      "readers": 0,
      "relevance": 9,
      "resulttype": "Journal Article",
      "subject": "symptoms, hypertension, age, susceptibility, severe cases",
      "tags": "Peer-reviewed",
      "title": "Host susceptibility to severe COVID-19 and establishment of a host risk score: findings of 487 cases outside Wuhan",
      "url": "https://ccforum.biomedcentral.com/track/pdf/10.1186/s13054-020-2833-7",
      "x": "0.406256560404283",
      "y": "0.110759287888353",
      "year": "2020-03-18"
    },
    {
      "area": "Host biology and clinical findings",
      "area_uri": 2,
      "authors": "Zhang, Peixun; Li, Jia; Liu, Huixin; Han, Na; Ju, Jiabao; Kou, Yuhui; Chen, Lei; Jiang, Mengxi; Pan, Feng; Zheng,  Yali; Gao, Zhancheng; Jiang, Baoguo",
      "cluster_labels": "15-year follow-up, 2019 novel coronavirus, 487 cases outside",
      "comments": "ARDS is the cause of hospitalizations for many respiratory infections. This studies long term clinical impact.",
      "id": "https://doi.org/10.1038/s41413-020-0084-5",
      "lang_detected": "english",
      "link": "https://www.nature.com/articles/s41413-020-0084-5.pdf?origin=ppub",
      "oa_state": 1,
      "paper_abstract": "The most severe sequelae after rehabilitation from SARS are femoral head necrosis and pulmonary fibrosis. We performed a 15-year follow-up on the lung and bone conditions of SARS patients. We evaluated the recovery from lung damage and femoral head necrosis in an observational cohort study of SARS patients using pulmonary CT scans, hip joint MRI examinations, pulmonary function tests and hip joint function questionnaires. Eighty medical staff contracted SARS in 2003. Two patients died of SARS, and 78 were enrolled in this study from August 2003 to March 2018. Seventy-one patients completed the 15-year follow-up. The percentage of pulmonary lesions on CT scans diminished from 2003 (9.40 ± 7.83)% to 2004 (3.20 ± 4.78)% (P < 0.001) and remained stable thereafter until 2018 (4.60 ± 6.37)%. Between 2006 and 2018, the proportion of patients with interstitial changes who had improved pulmonary function was lower than that of patients without lesions, as demonstrated by the one-second ratio (FEV1/FVC%, t = 2.21, P = 0.04) and mid-flow of maximum expiration (FEF25%–75%, t = 2.76, P = 0.01). The volume of femoral head necrosis decreased significantly from 2003 (38.83 ± 21.01)% to 2005 (30.38 ± 20.23)% (P = 0.000 2), then declined slowly from 2005 to 2013 (28.99 ± 20.59)% and plateaued until 2018 (25.52 ± 15.51)%. Pulmonary interstitial damage and functional decline caused by SARS mostly recovered, with a greater extent of recovery within 2 years after rehabilitation. Femoral head necrosis induced by large doses of steroid pulse therapy in SARS patients without lesions, as demonstrated by the one-second ratio (FEV1/FVC%, t = 2.21, P = 0.04) and mid-flow of maximum expiration (FEF25%–75%, t = 2.76, P = 0.01). The volume of femoral head necrosis decreased significantly from 2003 (38.83 ± 21.01)% to 2005 (30.38 ± 20.23)% (P = 0.000 2), then declined slowly from 2005 to 2013 (28.99 ± 20.59)% and plateaued until 2018 (25.52 ± 15.51)%. Pulmonary interstitial damage and functional decline caused by SARS mostly recovered, with a greater extent of recovery within 2 years after rehabilitation. Femoral head necrosis induced by large doses of steroid pulse therapy in SARS patients was not progressive and was partially reversible.",
      "published_in": "Bone Research",
      "readers": 0,
      "relevance": 10,
      "resulttype": "Journal Article",
      "subject": "Long term effects, Bone, lung",
      "tags": "Peer-reviewed",
      "title": "Long-term bone and lung consequences associated with hospital-acquired severe acute respiratory syndrome: a 15-year follow-up from a prospective cohort study",
      "url": "https://www.nature.com/articles/s41413-020-0084-5.pdf?origin=ppub",
      "x": "0.256263248920559",
      "y": "0.427382426539428",
      "year": "2020-02-14"
    },
    {
      "area": "Host biology and clinical findings",
      "area_uri": 2,
      "authors": "Li, Ci-Xiu; Li, Wei; Zhou, Jun; Zhang, Bing; Feng, Yan; Xu, Chang-Ping; Lu, Yi-Yu; Holmes, Edward C.; Shi, Mang",
      "cluster_labels": "Acute respiratory",
      "comments": "",
      "id": "https://doi.org/10.1038/s41598-020-60992-6",
      "lang_detected": "english",
      "link": "https://www.nature.com/articles/s41598-020-60992-6.pdf",
      "oa_state": 1,
      "paper_abstract": "The diversity of pathogens associated with acute respiratory infection (ARI) makes diagnosis challenging. Traditional pathogen screening tests have a limited detection range and provide little additional information. We used total RNA sequencing (“meta-transcriptomics”) to reveal the full spectrum of microbes associated with paediatric ARI. Throat swabs were collected from 48 paediatric ARI patients and 7 healthy controls. Samples were subjected to meta-transcriptomics to determine the presence and abundance of viral, bacterial, and eukaryotic pathogens, and to reveal mixed infections, pathogen genotypes/subtypes, evolutionary origins, epidemiological history, and antimicrobial resistance. We identified 11 RNA viruses, 4 DNA viruses, 4 species of bacteria, and 1 fungus. While most are known to cause ARIs, others, such as echovirus 6, are rarely associated with respiratory disease. Co-infection of viruses and bacteria and of multiple viruses were commonplace (9/48), with one patient harboring 5 different pathogens, and genome sequence data revealed large intra-species diversity. Expressed resistance against eight classes of antibiotic was detected, with those for MLS, Bla, Tet, Phe at relatively high abundance. In summary, we used a simple total RNA sequencing approach to reveal the complex polymicrobial infectome in ARI. This provided comprehensive and clinically informative information relevant to understanding respiratory disease.",
      "published_in": "Scientific Reports",
      "readers": 0,
      "relevance": 11,
      "resulttype": "Journal Article",
      "subject": "Coinfection, acute respiratory distress, ARDS, pneumonia",
      "tags": "Peer-reviewed",
      "title": "High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection",
      "url": "https://www.nature.com/articles/s41598-020-60992-6.pdf",
      "x": "-0.131756517278513",
      "y": "0.285488561782344",
      "year": "2020-03-03"
    },
    {
      "area": "Epidemiology",
      "area_uri": 4,
      "authors": "Yang, Chang Hoon; Jung, Hyejin",
      "cluster_labels": "2015 South Korea, 2019 coronavirus, Coronavirus 2019-ncov SARSCov2",
      "comments": "",
      "id": "https://doi.org/10.1038/s41598-020-61133-9",
      "lang_detected": "english",
      "link": "https://www.nature.com/articles/s41598-020-61133-9.pdf",
      "oa_state": 1,
      "paper_abstract": "Network analysis to examine infectious contact relations provides an important means to uncover the topologies of individual infectious contact networks. This study aims to investigate the spread of diseases among individuals over contact networks by exploring the 2015 Middle East Respiratory Syndrome (MERS) outbreak in Korea. We present several distinct features of MERS transmission by employing a comprehensive approach in network research to examine both the traced relationship matrix of infected individuals and their bipartite transmission routes among healthcare facilities visited for treatment. The results indicate that a few super-spreaders were more likely to hold certain structural advantages by linking to an exceptional number of other individuals, causing several ongoing transmission events in neighbourhoods without the aid of any intermediary. Thus, the infectious contact network exhibited small-world dynamics characterised by locally clustered contacts exposed to transmission paths via short path lengths. In addition, nosocomial infection analysis shows the pattern of a common-source outbreak followed by secondary person-to-person transmission of the disease. Based on the results, we suggest policy implications related to the redesign of prevention and control strategies against the spread of epidemics.",
      "published_in": "Scientific Reports",
      "readers": 0,
      "relevance": 12,
      "resulttype": "Journal Article",
      "subject": "South Korea, Mers, incidence, spread",
      "tags": "Peer-reviewed",
      "title": "Topological dynamics of the 2015 South Korea MERS-CoV spread-on-contact networks",
      "url": "https://www.nature.com/articles/s41598-020-61133-9.pdf",
      "x": "0.253108127651107",
      "y": "-0.124621775154876",
      "year": "2020-03-09"
    },
    {
      "area": "Host biology and clinical findings",
      "area_uri": 2,
      "authors": "Sun, Qin;  Qiu, Haibo; Huang, Mao; Yang, Yi.",
      "cluster_labels": "15-year follow-up, 2019 novel coronavirus, 487 cases outside",
      "comments": "",
      "id": "https://doi.org/10.1186/s13613-020-00650-2",
      "lang_detected": "english",
      "link": "https://annalsofintensivecare.springeropen.com/track/pdf/10.1186/s13613-020-00650-2",
      "oa_state": 1,
      "paper_abstract": "N/A",
      "published_in": "Annals of Intensive Care",
      "readers": 0,
      "relevance": 13,
      "resulttype": "Journal Article",
      "subject": "Intensive Care, ICU",
      "tags": "Peer-reviewed",
      "title": "Lower mortality of COVID-19 by early recognition and intervention: experience from Jiangsu Province",
      "url": "https://annalsofintensivecare.springeropen.com/track/pdf/10.1186/s13613-020-00650-2",
      "x": "0.479466467663354",
      "y": "-0.330253783369334",
      "year": "2020-03-18"
    },
    {
      "area": "Host biology and clinical findings",
      "area_uri": 2,
      "authors": "Havelka, Aleksandra; Sejersen, Kristina; Venge, Per; Pauksens,  Karlis; Larsson, Anders",
      "cluster_labels": "Acute respiratory",
      "comments": "",
      "id": "https://doi.org/10.1038/s41598-020-61094-z",
      "lang_detected": "english",
      "link": "https://www.nature.com/articles/s41598-020-61094-z.pdf",
      "oa_state": 1,
      "paper_abstract": "Respiratory tract infections require early diagnosis and adequate treatment. With the antibiotic overuse and increment in antibiotic resistance there is an increased need to accurately distinguish between bacterial and viral infections. We investigated the diagnostic performance of calprotectin in respiratory tract infections and compared it with the performance of heparin binding protein (HBP) and procalcitonin (PCT). Biomarkers were analyzed in patients with viral respiratory infections and patients with bacterial pneumonia, mycoplasma pneumonia and streptococcal tonsillitis (n = 135). Results were compared with values obtained from 144 healthy controls. All biomarkers were elevated in bacterial and viral infections compared to healthy controls. Calprotectin was significantly increased in patients with bacterial infections; bacterial pneumonia, mycoplasma pneumonia and streptococcal tonsillitis compared with viral infections. PCT was significantly elevated in patients with bacterial pneumonia compared to viral infections but not in streptococcal tonsillitis or mycoplasma caused infections. HBP was not able to distinguish between bacterial and viral causes of infections. The overall clinical performance of calprotectin in the distinction between bacterial and viral respiratory infections, including mycoplasma was greater than performance of PCT and HBP. Rapid determination of calprotectin may improve the management of respiratory tract infections and allow more precise diagnosis and selective use of antibiotics.",
      "published_in": "Scientific Reports",
      "readers": 0,
      "relevance": 14,
      "resulttype": "Journal Article",
      "subject": "Biomarker",
      "tags": "Peer-reviewed",
      "title": "Calprotectin, a new biomarker for diagnosis of acute respiratory infections",
      "url": "https://www.nature.com/articles/s41598-020-61094-z.pdf",
      "x": "-0.0116441682907959",
      "y": "0.292797232568418",
      "year": "2020-03-06"
    },
    {
      "area": "Host biology and clinical findings",
      "area_uri": 2,
      "authors": "Dai, Xiaofeng; Hakizimana, Olivier; Zhang, Xuanhao; Chandra Kaushik, Aman; Zhang, Jianying",
      "cluster_labels": "2019 Wuhan novel, 2019-ncov indicate evolutionary, Conserved functional regions",
      "comments": "",
      "id": "https://doi.org/10.1080/21505594.2020.1726594",
      "lang_detected": "english",
      "link": "https://www.tandfonline.com/doi/pdf/10.1080/21505594.2020.1726594?needAccess=true",
      "oa_state": 1,
      "paper_abstract": "With the high pervasiveness of viral diseases, the battle against viruses has never ceased. Here we discuss five cellular processes, namely “autophagy”, “programmed cell death”, “immune response”, “cell cycle alteration”, and “lipid metabolic reprogramming”, that considerably guide viral replication after host infection in an orchestrated manner. On viral infection, “autophagy” and “programmed cell death” are two dynamically synchronized cell survival programs; “immune response” is a cell defense program typically suppressed by viruses; “cell cycle alteration” and “lipid metabolic reprogramming” are two altered cell housekeeping programs tunable in both directions. We emphasize on their functionalities in modulating viral replication, strategies viruses have evolved to tune these processes for their benefit, and how these processes orchestrate and govern cell fate upon viral infection. Understanding how viruses hijack host networks has both academic and industrial values in providing insights toward therapeutic strategy design for viral disease control, offering useful information in applications that aim to use viral vectors to improve human health such as gene therapy, and providing guidelines to maximize viral particle yield for improved vaccine production at a reduced cost.",
      "published_in": "Virulence",
      "readers": 0,
      "relevance": 15,
      "resulttype": "Review",
      "subject": "GO Terms, omics",
      "tags": "Peer-reviewed",
      "title": "Orchestrated efforts on host network hijacking: Processes governing virus replication",
      "url": "https://www.tandfonline.com/doi/pdf/10.1080/21505594.2020.1726594?needAccess=true",
      "x": "-0.279037096581448",
      "y": "0.278950239019079",
      "year": "2020-02-16"
    },
    {
      "area": "Therapeutics",
      "area_uri": 3,
      "authors": "Rensi, Stefano; Altman, Russ B; Liu, Tianyun; Lo, Yu-Chen; McInnes, Greg; Derry, Alex; Keys, Allison",
      "cluster_labels": "2015 South Korea, 2019 coronavirus, Coronavirus 2019-ncov SARSCov2",
      "comments": "",
      "id": "https://doi.org/10.26434/chemrxiv.12009582",
      "lang_detected": "english",
      "link": "N/A",
      "oa_state": 1,
      "paper_abstract": "The most rapid path to discovering treatment options for the novel coronavirus SARS-CoV-2 is to find existing medications that are active against the virus. We have focused on identifying repurposing candidates for the transmembrane serine protease family member II (TMPRSS2), which is critical for entry of coronaviruses into cells. Using known 3D structures of close homologs, we created seven homology models. We also identified a set of serine protease inhibitor drugs, generated several conformations of each, and docked them into our models. We used three known chemical (non-drug) inhibitors and one validated inhibitor of TMPRSS2 in MERS as benchmark compounds and found six compounds with predicted high binding affinity in the range of the known inhibitors. We also showed that a previously published weak inhibitor, Camostat, had a significantly lower binding score than our six compounds. All six compounds are anticoagulants with significant and potentially dangerous clinical effects and side effects. Nonetheless, if these compounds significantly inhibit SARS-CoV-2 infection, they could represent a potentially useful clinical tool.",
      "published_in": "ChemRxiv",
      "readers": 0,
      "relevance": 16,
      "resulttype": "Preprint",
      "subject": "structural modeling, computational modeling",
      "tags": "Peer-reviewed",
      "title": "Homology Modeling of TMPRSS2 Yields Candidate Drugs That May Inhibit Entry of SARS-CoV-2 into Human Cells",
      "url": "N/A",
      "x": "-0.334841807501253",
      "y": "-0.138338021669793",
      "year": "2020-03-20"
    },
    {
      "area": "Host biology and clinical findings",
      "area_uri": 2,
      "authors": "Zhou, Bo; She, Jianqing; Wang, Yadan; Ma, Xiancang",
      "cluster_labels": "15-year follow-up, 2019 novel coronavirus, 487 cases outside",
      "comments": "",
      "id": "https://doi.org/10.21203/rs.3.rs-18079/v1",
      "lang_detected": "english",
      "link": "N/A",
      "oa_state": 1,
      "paper_abstract": "ObjectivesIt is of clinical significance to evaluate the disease severity and investigate possible biomarkers of 2019 Novel coronavirus disease (COVID-19). In this study, we aim to describe the clinical characteristics of infection makers in severe and very severe patients with COVID-19. MethodsThis is a single center, observational analysis. We enrolled 48 in-hospital severe patients with COVID-19 admitted to the West District of Union Hospital of Tongji Medical College and analyzed infection biomarkers in 20 patients who had been tested for ferritin, PCT, CRP, etc. ResultsThe median age was 59yrd (inter quartile range [IQR]:46-61) among severe COVID-19 group and 57yrd (IQR:45-71.5) among very severe group. We noted significantly increased CRP (1.48mg/L [IQR: 16.69-2.74] vs. 57.98mg/L [IQR: 38.335-77.565], P<0.05), PCT(0.05ng/ml [IQR: 0.03-0.06] vs. 0.21ng/ml [IQR: 0.11-0.42], P<0.05) and ferritin (291.13ng/ml [IQR: 102.1-648.42] vs. 1006.16ng/ml [IQR: 408.265-1988.25]). For blood count, significant increase was noticed in neutrophil percentage (67.6% [IQR: 61.8-76.4] vs. 86.7% [IQR: 82-92.35], P<0.01) and neutrophil count (3.75*10^9/L [IQR: 3.42-4.93] vs. 8.11*10^9/L [IQR: 5.675-8.905], P<0.05); and decrease was seen in lymphocyte percentage (22.7% [IQR: 17.4-27.4] vs. 8% [IQR: 4.85-13], P<0.05), lymphocyte count (1.62*10^9/L [IQR: 0.7-1.73] vs. 0.68*10^9/L [IQR: 0.385-1.04], P<0.05), and platelet count (214*10^9/L [IQR: 184-247] vs. 147*10^9/L [IQR: 126-202.5], P<0.05). ConclusionsThe serum levels of CRP, PCT and ferritin are markedly increased in very severe compared with severe COVID-19. Increased CRP, PCT and ferritin level might correlate to secondary bacterial infection and associated with poor clinical prognosis.",
      "published_in": "Research Square",
      "readers": 0,
      "relevance": 17,
      "resulttype": "Preprint",
      "subject": "COVID-19, Biomarkers, C-reactive protein, Ferritin, Procalcitonin",
      "tags": "Peer-reviewed",
      "title": "Utility of Ferritin, Procalcitonin, and C-reactive Protein in Severe Patients with 2019 Novel Coronavirus Disease",
      "url": "N/A",
      "x": "0.313879007124218",
      "y": "0.192346426757019",
      "year": "2020-03-19"
    },
    {
      "area": "Host biology and clinical findings",
      "area_uri": 2,
      "authors": "Totura, Allison; Livingston, Virginia; Frick, Ondraya; Dyer, David; Nichols, Donald; Nalca, Aysegul",
      "cluster_labels": "2015 South Korea, 2019 coronavirus, Coronavirus 2019-ncov SARSCov2",
      "comments": "",
      "id": "https://doi.org/10.21203/rs.3.rs-17952/v1",
      "lang_detected": "english",
      "link": "N/A",
      "oa_state": 1,
      "paper_abstract": "Emerging highly pathogenic coronaviruses (CoV) are a global public health threat due to the potential for person-to-person transmission and higher mortality rates than common seasonal respiratory pathogens. Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in 2012, causing lethal respiratory disease in approximately 35% of human cases. Primate models of highly pathogenic coronavirus infection are needed to support development of therapeutics or vaccines, but few models exist that recapitulate severe disease signs. For initial development of a MERS-CoV primate model, twelve African green monkeys (AGMs) were exposed to 103, 104, or 105 PFU target doses of aerosolized MERS-CoV. We observed a dose-dependent increase of respiratory disease signs and viral titers in serum and throat swabs between the 103 PFU and the 105 PFU dose groups, although all AGMs survived for the 28 day duration of the study. This study is the first to describe dose-dependent effects of highly pathogenic coronavirus infection of primates and uses a route of infection (small particle aerosol) with potential relevance to MERS-CoV transmission in humans. Aerosol exposure of AGMs may provide a platform for the development of primate models of novel coronavirus disease, with potential utility in therapeutic development and viral pathogenesis studies.",
      "published_in": "Research Square",
      "readers": 0,
      "relevance": 18,
      "resulttype": "Preprint",
      "subject": "coronavirus, CoV, Middle East respiratory syndrome, MERS, MERS-CoV, primate model, African green monkey, respiratory, aerosol, infectious disease, animal model, medical countermeasure, small particle aerosol",
      "tags": "Peer-reviewed",
      "title": "Small Particle Aerosol Exposure of African Green Monkeys to MERS-CoV as a Model for Highly Pathogenic Coronavirus Infection",
      "url": "N/A",
      "x": "-0.114761601297843",
      "y": "0.0118880505219303",
      "year": "2020-03-19"
    },
    {
      "area": "Therapeutics",
      "area_uri": 3,
      "authors": "Magar, Rishikesh; Yadav, Prakarsh; Barati Farimani, Amir",
      "cluster_labels": "2 infection diagnosis, Neutralizing antibodies Discovered, Combined antibody test",
      "comments": "",
      "id": "https://arxiv.org/abs/arXiv:2003.08447",
      "lang_detected": "english",
      "link": "https://arxiv.org/ftp/arxiv/papers/2003/2003.08447.pdf",
      "oa_state": 1,
      "paper_abstract": "The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. Recent outbreak of novel coronavirus infected and killed thousands of people in the world. Rapid methods in finding peptides or antibody sequences that can inhibit the viral epitopes of COVID-19 will save the life of thousands. In this paper, we devised a machine learning (ML) model to predict the possible inhibitory synthetic antibodies for Corona virus. We collected 1933 virus-antibody sequences and their clinical patient neutralization response and trained an ML model to predict the antibody response. Using graph featurization with variety of ML methods, we screened thousands of hypothetical antibody sequences and found 8 stable antibodies that potentially inhibit COVID-19. We combined bioinformatics, structural biology, and Molecular Dynamics (MD) simulations to verify the stability of the candidate antibodies that can inhibit the Corona virus.",
      "published_in": "ArXiv",
      "readers": 0,
      "relevance": 19,
      "resulttype": "Preprint",
      "subject": "Coronavirus, COVID-19, Machine Learning, Antibody Engineering, Bio-informatics, Structural Biology",
      "tags": "Peer-reviewed",
      "title": "Potential Neutralizing Antibodies Discovered for Novel Corona Virus Using Machine Learning",
      "url": "https://arxiv.org/ftp/arxiv/papers/2003/2003.08447.pdf",
      "x": "-0.224726646503094",
      "y": "-0.12178337970293",
      "year": "2020-03-18"
    },
    {
      "area": "Host biology and clinical findings",
      "area_uri": 2,
      "authors": "Blanco-Melo, Daniel; Nilsson-Payant, Benjamin; Liu, Wen-Chun; Moeller, Rasmus; Panis, Maryline; Sachs, David; Albrecht, Randy; tenOever, Benjamin R.",
      "cluster_labels": "2 infection diagnosis, Neutralizing antibodies Discovered, Combined antibody test",
      "comments": "",
      "id": "https://doi.org/10.1101/2020.03.24.004655",
      "lang_detected": "english",
      "link": "https://www.biorxiv.org/content/10.1101/2020.03.24.004655v1.full.pdf",
      "oa_state": 1,
      "paper_abstract": "One of the greatest threats to humanity is the emergence of a pandemic virus. Among those with the greatest potential for such an event include influenza viruses and coronaviruses. In the last century alone, we have observed four major influenza A virus pandemics as well as the emergence of three highly pathogenic coronaviruses including SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic. As no effective antiviral treatments or vaccines are presently available against SARS-CoV-2, it is important to understand the host response to this virus as this may guide the efforts in development towards novel therapeutics. Here, we offer the first in-depth characterization of the host transcriptional response to SARS-CoV-2 and other respiratory infections through in vitro, ex vivo, and in vivo model systems. Our data demonstrate the each virus elicits both core antiviral components as well as unique transcriptional footprints. Compared to the response to influenza A virus and respiratory syncytial virus, SARS-CoV-2 elicits a muted response that lacks robust induction of a subset of cytokines including the Type I and Type III interferons as well as a numerous chemokines. Taken together, these data suggest that the unique transcriptional signature of this virus may be responsible for the development of COVID-19.",
      "published_in": "BoioRxiv",
      "readers": 0,
      "relevance": 20,
      "resulttype": "Preprint",
      "subject": "COVID-19, transcriptomics, in vitro, in vivo, ex vivo",
      "tags": "N/A",
      "title": "SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems",
      "url": "https://www.biorxiv.org/content/10.1101/2020.03.24.004655v1.full.pdf",
      "x": "-0.254335152969548",
      "y": "0.0585490624124536",
      "year": "2020-03-24"
    },
    {
      "area": "Immunity",
      "area_uri": 5,
      "authors": "Bao, Linlin; Deng, Wei; Gao, Hong; Xiao, Chong; Liu, Jiayi; Xue, Jing; Lv, Qi; Liu, Jiangning; Yu, Pin; Xu, Yanfeng; Qi, Feifei; Qu, Yajin; Li, Fengdi; Xiang, Zhiguang; Yu, Haisheng; Gong, Shuran; Liu, Mingya; Wang, Guanpeng; Wang, Shunyi; Song, Zhiqi; Zhao, Wenjie; Han, Yunlin; Zhao, Linna; Liu, Xing; Wei,  Qiang; Qin, Chuan",
      "cluster_labels": "2 infection diagnosis, Neutralizing antibodies Discovered, Combined antibody test",
      "comments": "",
      "id": "https://www.biorxiv.org/content/10.1101/2020.03.13.990226v1",
      "lang_detected": "english",
      "link": "https://www.biorxiv.org/content/biorxiv/early/2020/03/14/2020.03.13.990226.full.pdf",
      "oa_state": 1,
      "paper_abstract": "An outbreak of the Corona Virus Disease 2019 (COVID-19), caused by the severe acute respiratory syndrome CoV-2 (SARS-CoV-2), began in Wuhan and spread globally. Recently, it has been reported that discharged patients in China and elsewhere were testing positive after recovering. However, it remains unclear whether the convalescing patients have a risk of “relapse” or “reinfection”. The longitudinal tracking of re-exposure after the disappeared symptoms of the SARS-CoV-2-infected monkeys was performed in this study. We found that weight loss in some monkeys, viral replication mainly in nose, pharynx, lung and gut, as well as moderate interstitial pneumonia at 7 days post-infection (dpi) were clearly observed in rhesus monkeys after the primary infection. After the symptoms were alleviated and the specific antibody tested positively, the half of infected monkeys were rechallenged with the same dose of SARS-CoV-2 strain. Notably, neither viral loads in nasopharyngeal and anal swabs along timeline nor viral replication in all primary tissue compartments at 5 days post-reinfection (dpr) was found in re-exposed monkeys. Combined with the follow-up virologic, radiological and pathological findings, the monkeys with re-exposure showed no recurrence of COVID-19, similarly to the infected monkey without rechallenge. Taken together, our results indicated that the primary SARS-CoV-2 infection could protect from subsequent exposures, which have the reference of prognosis of the disease and vital implications for vaccine design.",
      "published_in": "BioRxiv",
      "readers": 0,
      "relevance": 21,
      "resulttype": "Preprint",
      "subject": "rhesus macaque, immune memory, COVID-19",
      "tags": "",
      "title": "Reinfection could not occur in SARS-CoV-2 infected rhesus macaques",
      "url": "https://www.biorxiv.org/content/biorxiv/early/2020/03/14/2020.03.13.990226.full.pdf",
      "x": "0.0505716044030282",
      "y": "0.142546333554966",
      "year": "2020-03-14"
    },
    {
      "area": "Epidemiology",
      "area_uri": 4,
      "authors": "Wu, Joseph T; Leung, Kath; Leung, Gabriel M",
      "cluster_labels": "2 SARSCov2 epidemic, 2019-ncov outbreak originating, 21st century GIS",
      "comments": "",
      "id": "https://doi.org/10.1016/S0140-6736(20)30260-9",
      "lang_detected": "english",
      "link": "https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930260-9",
      "oa_state": 2,
      "paper_abstract": "Background Since Dec 31, 2019, the Chinese city of Wuhan has reported an outbreak of atypical pneumonia caused by the 2019 novel coronavirus (2019-nCoV). Cases have been exported to other Chinese cities, as well as internationally, threatening to trigger a global outbreak. Here, we provide an estimate of the size of the epidemic in Wuhan on the basis of the number of cases exported from Wuhan to cities outside mainland China and forecast the extent of the domestic and global public health risks of epidemics, accounting for social and non-pharmaceutical prevention interventions. Methods We used data from Dec 31, 2019, to Jan 28, 2020, on the number of cases exported from Wuhan internationally (known days of symptom onset from Dec 25, 2019, to Jan 19, 2020) to infer the number of infections in Wuhan from Dec 1, 2019, to Jan 25, 2020. Cases exported domestically were then estimated. We forecasted the national and global spread of 2019-nCoV, accounting for the effect of the metropolitan-wide quarantine of Wuhan and surrounding cities, which began Jan 23–24, 2020. We used data on monthly flight bookings from the Official Aviation Guide and data on human mobility across more than 300 prefecture-level cities in mainland China from the Tencent database. Data on confirmed cases were obtained from the reports published by the Chinese Center for Disease Control and Prevention. Serial interval estimates were based on previous studies of severe acute respiratory syndrome coronavirus (SARS-CoV). A susceptible-exposed-infectious-recovered metapopulation model was used to simulate the epidemics across all major cities in China. The basic reproductive number was estimated using Markov Chain Monte Carlo methods and presented using the resulting posterior mean and 95% credibile interval (CrI).Findings In our baseline scenario, we estimated that the basic reproductive number for 2019-nCoV was 2·68 (95% CrI 2·47–2·86) and that 75 815 individuals (95% CrI 37 304–130 330) have been infected in Wuhan as of Jan 25, 2020. The epidemic doubling time was 6·4 days (95% CrI 5·8–7·1). We estimated that in the baseline scenario, Chongqing, Beijing, Shanghai, Guangzhou, and Shenzhen had imported 461 (95% CrI 227–805), 113 (57–193), 98 (49–168), 111 (56–191), and 80 (40–139) infections from Wuhan, respectively. If the transmissibility of 2019-nCoV were similar everywhere domestically and over time, we inferred that epidemics are already growing exponentially in multiple major cities of China with a lag time behind the Wuhan outbreak of about 1–2 weeks. Interpretation Given that 2019-nCoV is no longer contained within Wuhan, other major Chinese cities are probably sustaining localised outbreaks. Large cities overseas with close transport links to China could also become outbreak epicentres, unless substantial public health interventions at both the population and personal levels are implemented immediately. Independent self-sustaining outbreaks in major cities globally could become inevitable because of substantial exportation of presymptomatic cases and in the absence of large-scale public health interventions. Preparedness plans and mitigation interventions should be readied for quick deployment globally",
      "published_in": "The Lancet",
      "readers": 0,
      "relevance": 22,
      "resulttype": "Journal Article",
      "subject": "Forecast",
      "tags": "Peer-reviewed",
      "title": "Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study",
      "url": "https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820%2930260-9",
      "x": "0.082013811976832",
      "y": "-0.236751025702442",
      "year": "2020-01-31"
    },
    {
      "area": "Diagnostics",
      "area_uri": 6,
      "authors": "Li,  Zhengtu; Yi, Yongxiang; Luo, Xiaomei; Xiong, Nian; Liu, Yang; Li, Shaoqiang; Sun, Ruilin; Wang,Yanqun; Hu, Bicheng; Chen, Wei; Zhang, Yongchen; Wang, Jing; Huang, Baofu; Lin, Ye; Yang, Jiasheng; Cai, Wensheng; Wang,  Xuefeng; Cheng, Jing; Chen, Zhiqiang; Sun, Kangjun; Pan, Weimin; Zhan, Zhifei; Chen, Liyan; Ye, Feng",
      "cluster_labels": "2 infection diagnosis, Neutralizing antibodies Discovered, Combined antibody test",
      "comments": "",
      "id": "https://doi.org/10.1002/jmv.25727",
      "lang_detected": "english",
      "link": "https://onlinelibrary.wiley.com/doi/epdf/10.1002/jmv.25727",
      "oa_state": 3,
      "paper_abstract": "The outbreak of the novel coronavirus disease (COVID‐19) quickly spread all over China and to more than 20 other countries. Although the virus (SARS‐Cov‐2) nucleic acid RT‐PCR test has become the standard method for diagnosis of SARS‐CoV‐2 infection, these real‐time PCR test kits have many limitations. In addition, high false negative rates were reported. There is an urgent need for an accurate and rapid test method to quickly identify large number of infected patients and asymptomatic carriers to prevent virus transmission and assure timely treatment of patients. We have developed a rapid and simple point‐of‐care lateral flow immunoassay which can detect IgM and IgG antibodies simultaneously against SARS‐CoV‐2 virus in human blood within 15 minutes which can detect patients at different infection stages. With this test kit, we carried out clinical studies to validate its clinical efficacy uses. The clinical detection sensitivity and specificity of this test were measured using blood samples collected from 397 PCR confirmed COVID‐19 patients and 128 negative patients at 8 different clinical sites. The overall testing sensitivity was 88.66% and specificity was 90.63%. In addition, we evaluated clinical diagnosis results obtained from different types of venous and fingerstick blood samples. The results indicated great detection consistency among samples from fingerstick blood, serum and plasma of venous blood. The IgM‐IgG combined assay has better utility and sensitivity compared with a single IgM or IgG test. It can be used for the rapid screening of SARS‐CoV‐2 carriers, symptomatic or asymptomatic, in hospitals, clinics, and test laboratories.",
      "published_in": "Journal of Medical Virology",
      "readers": 0,
      "relevance": 23,
      "resulttype": "Journal Article",
      "subject": "COVID-19",
      "tags": "Peer-reviewed",
      "title": "Development and Clinical Application of A Rapid IgM‐IgG Combined Antibody Test for SARS‐CoV‐2 Infection Diagnosis",
      "url": "https://onlinelibrary.wiley.com/doi/epdf/10.1002/jmv.25727",
      "x": "0.0741275645505697",
      "y": "0.0681161501140251",
      "year": "2020-02-27"
    },
    {
      "area": "Viral biology",
      "area_uri": 1,
      "authors": "van Doremalen, Neeltje; Morris, Dylan H.; Holbrook, Myndi G.; Gamble, Amandine; Williamson, Brandi N.; Tamin, Azaibi; Harcourt, Jennifer L.; Thornburg, Natalie J.;Gerber, Susan I.; Lloyd-Smith, James O.; de Wit, Emmie; Munster, Vincent J.",
      "cluster_labels": "15-year follow-up, 2019 novel coronavirus, 487 cases outside",
      "comments": "One of multiple studies",
      "id": "https://www.nejm.org/doi/10.1056/NEJMc2004973",
      "lang_detected": "english",
      "link": "https://www.nejm.org/doi/pdf/10.1056/NEJMc2004973?articleTools=true",
      "oa_state": 2,
      "paper_abstract": "N/A",
      "published_in": "The New England Journal of Medicine",
      "readers": 0,
      "relevance": 24,
      "resulttype": "Journal Article",
      "subject": "SARS-COV, COVID-19, Stability, Aerosol, Surface",
      "tags": "Peer-reviewed",
      "title": "Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1",
      "url": "https://www.nejm.org/doi/pdf/10.1056/NEJMc2004973?articleTools=true",
      "x": "0.448460407263523",
      "y": "-0.105276285141803",
      "year": "2020-03-17"
    },
    {
      "area": "Epidemiology",
      "area_uri": 4,
      "authors": "Li, Ruiyun; Pei, Sen; Chen, Bin; Song, Yimeng; Zhang, Tao; Yang, Wan; Shaman, Jeffrey",
      "cluster_labels": "2 infection diagnosis, Neutralizing antibodies Discovered, Combined antibody test",
      "comments": "Many studies describe dissemination from asymptomatic people.",
      "id": "https://science.sciencemag.org/content/early/2020/03/24/science.abb3221",
      "lang_detected": "english",
      "link": "https://science.sciencemag.org/content/early/2020/03/24/science.abb3221.full.pdf",
      "oa_state": 2,
      "paper_abstract": "Estimation of the prevalence and contagiousness of undocumented novel coronavirus (SARS-CoV2) infections is critical for understanding the overall prevalence and pandemic potential of this disease. Here we use observations of reported infection within China, in conjunction with mobility data, a networked dynamic metapopulation model and Bayesian inference, to infer critical epidemiological characteristics associated with SARS-CoV2, including the fraction of undocumented infections and their contagiousness. We estimate 86% of all infections were undocumented (95% CI: [82%–90%]) prior to 23 January 2020 travel restrictions. Per person, the transmission rate of undocumented infections was 55% of documented infections ([46%–62%]), yet, due to their greater numbers, undocumented infections were the infection source for 79% of documented cases. These findings explain the rapid geographic spread of SARS-CoV2 and indicate containment of this virus will be particularly challenging.",
      "published_in": "Science",
      "readers": 0,
      "relevance": 25,
      "resulttype": "Journal Article",
      "subject": "COVID-19, risk, dissemination",
      "tags": "Peer-reviewed",
      "title": "Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2)",
      "url": "https://science.sciencemag.org/content/early/2020/03/24/science.abb3221.full.pdf",
      "x": "-0.00872944291551294",
      "y": "0.0567744827547777",
      "year": "2020-03-16"
    },
    {
      "area": "Diagnostics",
      "area_uri": 6,
      "authors": "Sheridan, Cormac",
      "cluster_labels": "2 SARSCov2 epidemic, 2019-ncov outbreak originating, 21st century GIS",
      "comments": "",
      "id": "https://www.nature.com/articles/d41587-020-00002-2",
      "lang_detected": "english",
      "link": "N/A",
      "oa_state": 2,
      "paper_abstract": "N/A",
      "published_in": "Nature Biotechnology",
      "readers": 0,
      "relevance": 26,
      "resulttype": "Journal Article",
      "subject": "Collaboration",
      "tags": "Perspective",
      "title": "Coronavirus and the race to distribute reliable diagnostics International teams worked at speed to make tests for the virus available in record time.",
      "url": "N/A",
      "x": "-0.128270126874195",
      "y": "-0.482202121725181",
      "year": "2020-02-21"
    },
    {
      "area": "Host biology and clinical findings",
      "area_uri": 2,
      "authors": "Akin, Joe",
      "cluster_labels": "Acute respiratory",
      "comments": "Explores the biology underlying bacterial superinfection",
      "id": "https://refigure.org/collections/item/7e5f9f50-5744-11ea-8c54-9323bc73fc6b/",
      "lang_detected": "english",
      "link": "N/A",
      "oa_state": 3,
      "paper_abstract": "Opportunistic bacterial pneumonia following viral infection of the lower respiratory tract is a significant cause of mortality in flu and, possibly, coronavirus. Here I show a prevailing model where possible overproduction of type I interferon, as a consequence of viral infection, creates a window of opportunity for bacterial colonization and growth. This window of opportunity is correlated, interestingly, with an increase in IP-10/CXCL10 chemokine, which is known for its ability to recruit virus-specific antigen-experienced T cells (in so called push-pull immunity). In the second figure, we see historical data on bacterial superinfection over flu seasons going back to 1890. Interestingly, while anecdotal reports indicate bacterial superinfection might be important in coronavirus, a few reports indicate SARS virus does not elicit type I interferon in human cells. Also, along these lines, we see a representative lung CT of a patient with the viral pneumonia often reported in patients with COVID-19 that included ground-glass opacities (GGO, indicated by arrows), described as a type of interstitial pneumonia. Due to the nature of the crises, data is being published and updated almost daily. It is unclear what percentage of patients succumb to the interstitial pneumonia and which succumb to opportunistic bacterial superinfection. At the same time, there are reports of patients being treated with antibiotics, presumably to prevent opportunistic bacterial infection. If beta-coronavirus infection has a distinct pathology, that does not, or rarely leads to bacterial pneumonia, antibiotics might not be as necessary as initially thought. I will continue to update this ReFigure as more information comes out in human patients and pre-clinical models.",
      "published_in": "ReFigure",
      "readers": 0,
      "relevance": 27,
      "resulttype": "ReFigure",
      "subject": "Bacteria, pneumonia, mortality, survival",
      "tags": "Collection",
      "title": "Coronavirus mortality as a consequence of bacterial superinfection",
      "url": "N/A",
      "x": "-0.0117486632224463",
      "y": "0.292743194658033",
      "year": "2020-03-26"
    },
    {
      "area": "Therapeutics",
      "area_uri": 3,
      "authors": "Akin, Joe",
      "cluster_labels": "Acute respiratory",
      "comments": "The first drug to achieve accelerated approval. But questions remain about safety and efficacy",
      "id": "https://refigure.org/collections/item/07cd6fa0-7050-11ea-8c54-9323bc73fc6b/",
      "lang_detected": "english",
      "link": "N/A",
      "oa_state": 3,
      "paper_abstract": "This ReFigure shows the results of two trials with hydroxycholorquine (HCQ) in COVID-19 patients. The first was conducted in France with HCQ and is a single-arm study on 26 patients. The second is a randomized control trial in Shanghai enrolling 30 patients using HCQ in the treatment arm. Both studies looked at similar time points for clearance of virus. While the first study suggested a dramatic reduction of virus after drug treatment, the second study did not confirm this. There are important differences between the studies. It looks like azithromycin was used in some patients for opportunistic bacterial infection, while in the second study it is unclear if antibiotics were used in some patients. Bacterial superinfection is often a concern with viral infection in the lower respiratory tract, while it is yet unclear whether this is a consequence of SARS-CoV-2 infection as for other common viral infections (see https://refigure.org/collections/item/7e5f9f50-5744-11ea-8c54-9323bc73fc6b/). Also, in the first study the dose used was higher at 600 mg (versus 400 mg in the second study). Thank you to Dr. Amy Williams for reviewing this with me and highlighting the differences between the two studies.",
      "published_in": "ReFigure",
      "readers": 0,
      "relevance": 28,
      "resulttype": "ReFigure",
      "subject": "COVID-19, HCQ, therapeutic",
      "tags": "Collection",
      "title": "Two trials evaluating hydroxycholorquine in COVID-19 patients",
      "url": "N/A",
      "x": "0.0846545164966574",
      "y": "0.226458699380659",
      "year": "2020-03-27"
    }
  ],
  "errors": [
    {
      "Abstract": "To test the API",
      "Access": "",
      "Area": "",
      "Authors": "Author, Test",
      "Comments": "",
      "ID": "https://invalid.url",
      "Keywords": "",
      "Link to PDF": "N/A",
      "Publication Date": "2020-04-06",
      "Publication Venue": "No publication venue",
      "Ready for inclusion in map?": "yes",
      "Tags": "",
      "Title": "This is a test entry",
      "Type": "Preprint",
      "reason": "{row: 31, column: \"Access\"}: \"\" is not in the list of legal options (open, closed, unknown, free)"
    }
  ]
}