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  1. Article ; Online: Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing.

    Levine, Zoë C / Sene, Aita / Mkandawire, Winnie / Deme, Awa B / Ndiaye, Tolla / Sy, Mouhamad / Gaye, Amy / Diedhiou, Younouss / Mbaye, Amadou M / Ndiaye, Ibrahima M / Gomis, Jules / Ndiop, Médoune / Sene, Doudou / Faye Paye, Marietou / MacInnis, Bronwyn L / Schaffner, Stephen F / Park, Daniel J / Badiane, Aida S / Colubri, Andres /
    Ndiaye, Mouhamadou / Sy, Ngayo / Sabeti, Pardis C / Ndiaye, Daouda / Siddle, Katherine J

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 747

    Abstract: The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical ... ...

    Abstract The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata in a cross-sectional study of febrile patients and healthy controls in a low malaria burden area. Using 16S and untargeted sequencing, we detected viral, bacterial, or eukaryotic pathogens in 23% (38/163) of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15.5% and 3.8% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model that can distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs (F1 score: 0.823). These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
    MeSH term(s) Humans ; Senegal/epidemiology ; Cross-Sectional Studies ; Malaria/diagnosis ; Malaria/epidemiology ; Plasmodium ; Fever/epidemiology ; Borrelia/genetics
    Language English
    Publishing date 2024-01-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-44800-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins.

    Srinivasan, Suhas / Cui, Hongzhu / Gao, Ziyang / Liu, Ming / Lu, Senbao / Mkandawire, Winnie / Narykov, Oleksandr / Sun, Mo / Korkin, Dmitry

    Viruses

    2020  Volume 12, Issue 4

    Abstract: During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand lives. However, the swiftly spreading virus also caused ...

    Abstract During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand 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 leveraged data about the related coronaviruses that is readily available in public databases and integrated these data into a single computational pipeline. As a result, we provide comprehensive structural genomics and interactomics roadmaps of SARS-CoV-2 and use this information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community.
    MeSH term(s) Animals ; Betacoronavirus/chemistry ; Betacoronavirus/genetics ; Binding Sites ; Biological Evolution ; COVID-19 ; Chiroptera/virology ; Computational Biology ; Conserved Sequence ; Coronavirus Infections ; Coronavirus Nucleocapsid Proteins ; Genome, Viral ; Genomics ; Humans ; Ligands ; Models, Molecular ; Nucleocapsid Proteins/chemistry ; Pandemics ; Phosphoproteins ; Phylogeny ; Pneumonia, Viral ; Protein Interaction Mapping ; Protein Structure, Tertiary ; SARS Virus ; SARS-CoV-2 ; Sequence Alignment ; Spike Glycoprotein, Coronavirus/chemistry ; Viral Envelope Proteins/chemistry ; Viral Matrix Proteins/chemistry ; Viral Proteins/genetics
    Chemical Substances Coronavirus Nucleocapsid Proteins ; Ligands ; Nucleocapsid Proteins ; Phosphoproteins ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins ; Viral Matrix Proteins ; Viral Proteins ; nucleocapsid phosphoprotein, SARS-CoV-2 ; spike protein, SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-03-25
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v12040360
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Improving diagnosis of non-malarial fevers in Senegal:

    Levine, Zoë C / Sene, Aita / Mkandawire, Winnie / Deme, Awa B / Ndiaye, Tolla / Sy, Mouhamad / Gaye, Amy / Diedhiou, Younouss / Mbaye, Amadou M / Ndiaye, Ibrahima / Gomis, Jules / Ndiop, Médoune / Sene, Doudou / Paye, Marietou Faye / MacInnis, Bronwyn / Schaffner, Stephen F / Park, Daniel J / Badiane, Aida S / Colubri, Andres /
    Ndiaye, Mouhamadou / Sy, Ngayo / Sabeti, Pardis C / Ndiaye, Daouda / Siddle, Katherine J

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical ... ...

    Abstract The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata from febrile patients and healthy controls in a low malaria burden area. Using 16S and unbiased sequencing, we detected viral, bacterial, or eukaryotic pathogens in 29% of NMFI cases. Bacteria were the most common, with relapsing fever
    Language English
    Publishing date 2023-08-25
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.08.24.23294564
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins

    Srinivasan, Suhas / Cui, Hongzhu / Gao, Ziyang / Liu, Ming / Lu, Senbao / Mkandawire, Winnie / Narykov, Oleksandr / Sun, Mo / Korkin, Dmitry

    Viruses

    Abstract: During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand lives However, the swiftly spreading virus also caused ... ...

    Abstract During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand 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 leveraged data about the related coronaviruses that is readily available in public databases and integrated these data into a single computational pipeline As a result, we provide comprehensive structural genomics and interactomics roadmaps of SARS-CoV-2 and use this information to infer the possible functional differences and similarities with the related SARS coronavirus All data are made publicly available to the research community
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #14753
    Database COVID19

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  5. Article ; Online: Structural genomics and interactomics of 2019 Wuhan novel coronavirus, 2019-nCoV, indicate evolutionary conserved functional regions of viral proteins

    Cui, Hongzhu / Gao, Ziyang / Liu, Ming / Lu, Senbao / Mo, Sun / Mkandawire, Winnie / Narykov, Oleksandr / Srinivasan, Suhas / Korkin, Dmitry

    bioRxiv

    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 ... ...

    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
    Keywords covid19
    Publisher BioRxiv; MedRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.02.10.942136
    Database COVID19

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    Inter-library loan at ZB MED

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  6. Article ; Online: Structural genomics and interactomics of 2019 Wuhan novel coronavirus, 2019-nCoV, indicate evolutionary conserved functional regions of viral proteins

    Cui, Hongzhu / Gao, Ziyang / Liu, Ming / Lu, Senbao / Mo, Sun / Mkandawire, Winnie / Narykov, Oleksandr / Srinivasan, Suhas / Korkin, Dmitry

    bioRxiv

    Keywords covid19
    Language English
    Publishing date 2020-02-14
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.02.10.942136
    Database COVID19

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    Inter-library loan at ZB MED

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  7. Article ; Online: Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins

    Srinivasan, Suhas / Cui, Hongzhu / Gao, Ziyang / Liu, Ming / Lu, Senbao / Mkandawire, Winnie / Narykov, Oleksandr / Sun, Mo / Korkin, Dmitry

    Viruses, 12(4):360

    2020  

    Abstract: During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand lives. However, the swiftly spreading virus also caused ...

    Abstract During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand 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 leveraged data about the related coronaviruses that is readily available in public databases and integrated these data into a single computational pipeline. As a result, we provide comprehensive structural genomics and interactomics roadmaps of SARS-CoV-2 and use this information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community.
    Keywords COVID-19 ; interactome ; 2019-nCoV ; 2019 novel coronavirus ; structural genomics ; protein-protein interactions ; SARS-CoV-2 ; covid19
    Language English
    Publishing country de
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  8. Article ; Online: Training community healthcare workers on the use of information and communication technologies: a randomised controlled trial of traditional versus blended learning in Malawi, Africa.

    Mastellos, Nikolaos / Tran, Tammy / Dharmayat, Kanika / Cecil, Elizabeth / Lee, Hsin-Yi / Wong, Cybele C Peng / Mkandawire, Winnie / Ngalande, Emmanuel / Wu, Joseph Tsung-Shu / Hardy, Victoria / Chirambo, Baxter Griphin / O'Donoghue, John Martin

    BMC medical education

    2018  Volume 18, Issue 1, Page(s) 61

    Abstract: Background: Despite the increasing uptake of information and communication technologies (ICT) within healthcare services across developing countries, community healthcare workers (CHWs) have limited knowledge to fully utilise computerised clinical ... ...

    Abstract Background: Despite the increasing uptake of information and communication technologies (ICT) within healthcare services across developing countries, community healthcare workers (CHWs) have limited knowledge to fully utilise computerised clinical systems and mobile apps. The 'Introduction to Information and Communication Technology and eHealth' course was developed with the aim to provide CHWs in Malawi, Africa, with basic knowledge and computer skills to use digital solutions in healthcare delivery. The course was delivered using a traditional and a blended learning approach.
    Methods: Two questionnaires were developed and tested for face validity and reliability in a pilot course with 20 CHWs. Those were designed to measure CHWs' knowledge of and attitudes towards the use of ICT, before and after each course, as well as their satisfaction with each learning approach. Following validation, a randomised controlled trial was conducted to assess the effectiveness of the two learning approaches. A total of 40 CHWs were recruited, stratified by position, gender and computer experience, and allocated to the traditional or blended learning group using block randomisation. Participants completed the baseline and follow-up questionnaires before and after each course to assess the impact of each learning approach on their knowledge, attitudes, and satisfaction. Per-item, pre-post and between-group, mean differences for each approach were calculated using paired and unpaired t-tests, respectively. Per-item, between-group, satisfaction scores were compared using unpaired t-tests.
    Results: Scores across all scales improved after attending the traditional and blended learning courses. Self-rated ICT knowledge was significantly improved in both groups with significant differences between groups in seven domains. However, actual ICT knowledge scores were similar across groups. There were no significant differences between groups in attitudinal gains. Satisfaction with the course was generally high in both groups. However, participants in the blended learning group found it more difficult to follow the content of the course.
    Conclusions: This study shows that there is no difference between blended and traditional learning in the acquisition of actual ICT knowledge among community healthcare workers in developing countries. Given the human resource constraints in remote resource-poor areas, the blended learning approach may present an advantageous alternative to traditional learning.
    MeSH term(s) Adult ; Attitude to Computers ; Cell Phone ; Community Health Workers/education ; Computers, Handheld ; Female ; Humans ; Information Technology ; Malawi ; Male ; Medical Informatics/education ; Middle Aged ; Reproducibility of Results ; Surveys and Questionnaires ; Telemedicine
    Language English
    Publishing date 2018-04-02
    Publishing country England
    Document type Journal Article ; Randomized Controlled Trial
    ZDB-ID 2044473-4
    ISSN 1472-6920 ; 1472-6920
    ISSN (online) 1472-6920
    ISSN 1472-6920
    DOI 10.1186/s12909-018-1175-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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