Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria

[1]  F. Aarestrup,et al.  Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage , 2023, FEMS microbes.

[2]  Pardis C Sabeti,et al.  Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria , 2023, Nature Communications.

[3]  Y. Yazdanpanah,et al.  Clinical characteristics of ambulatory and hospitalized patients with monkeypox virus infection: an observational cohort study , 2022, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[4]  Lily A. Chylek,et al.  Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework , 2022, Med.

[5]  S. Greenland,et al.  Causal Directed Acyclic Graphs. , 2022, JAMA.

[6]  C. Ihekweazu,et al.  Pathogens that Cause Illness Clinically Indistinguishable from Lassa Fever, Nigeria, 2018 , 2022, Emerging infectious diseases.

[7]  Ya-Chu Yu,et al.  Review of human pegivirus: Prevalence, transmission, pathogenesis, and clinical implication , 2022, Virulence.

[8]  M. Kraemer,et al.  Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa , 2021, Nature.

[9]  M. Beale,et al.  SARS-CoV-2 genomics as a springboard for future disease mitigation in LMICs , 2021, Nature reviews. Microbiology.

[10]  R. Pandey,et al.  Co-infections as Modulators of Disease Outcome: Minor Players or Major Players? , 2021, Frontiers in Microbiology.

[11]  A. Rebai,et al.  A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa , 2021, medRxiv.

[12]  Chuan-Xi Zhang,et al.  Novel Dicistroviruses in an Unexpected Wide Range of Invertebrates , 2021, Food and Environmental Virology.

[13]  Sergei L. Kosakovsky Pond,et al.  Detection of a SARS-CoV-2 variant of concern in South Africa , 2021, Nature.

[14]  D. Pajkrt,et al.  World-Wide Prevalence and Genotype Distribution of Enteroviruses , 2021, Viruses.

[15]  Samuel Alizon Superspreading genomes , 2021, Science.

[16]  A. Sigal,et al.  Sixteen novel lineages of SARS-CoV-2 in South Africa , 2021, Nature Medicine.

[17]  J. Derisi,et al.  Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids , 2020, Nature Medicine.

[18]  E. Holmes,et al.  Author Correction: A new coronavirus associated with human respiratory disease in China , 2020, Nature.

[19]  U. Dalrymple,et al.  Quantifying the incidence of severe-febrile-illness hospital admissions in sub-Saharan Africa , 2019, PloS one.

[20]  C. Chiu,et al.  Clinical metagenomics , 2019, Nature Reviews Genetics.

[21]  Pardis C Sabeti,et al.  Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria , 2019, Scientific Reports.

[22]  David K. Yang,et al.  Capturing sequence diversity in metagenomes with comprehensive and scalable probe design , 2019, Nature Biotechnology.

[23]  Wei Gu,et al.  Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection. , 2019, Annual Review of Pathology.

[24]  M. A. Suchard,et al.  Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak , 2019, Science.

[25]  M. Docquier,et al.  Detection of dicistroviruses RNA in blood of febrile Tanzanian children , 2019, Emerging microbes & infections.

[26]  A. Barrett The reemergence of yellow fever , 2018, Science.

[27]  Tulio de Oliveira,et al.  Genome Detective: an automated system for virus identification from high-throughput sequencing data , 2018, Bioinform..

[28]  Pardis C Sabeti,et al.  Field validation of recombinant antigen immunoassays for diagnosis of Lassa fever , 2018, Scientific Reports.

[29]  E. Delwart,et al.  Sera of Peruvians with fever of unknown origins include viral nucleic acids from non-vertebrate hosts , 2018, Virus Genes.

[30]  A. Djikeng,et al.  Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus , 2017, Virology Journal.

[31]  D. Espósito,et al.  Sensitivity and detection of chikungunya viral genetic material using several PCR-based approaches. , 2017, Revista da Sociedade Brasileira de Medicina Tropical.

[32]  A. von Haeseler,et al.  UFBoot2: Improving the Ultrafast Bootstrap Approximation , 2017, bioRxiv.

[33]  M. Groschup,et al.  A Novel Pan-Flavivirus Detection and Identification Assay Based on RT-qPCR and Microarray , 2017, BioMed research international.

[34]  Thomas K. F. Wong,et al.  ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates , 2017, Nature Methods.

[35]  Anh-Minh A. Tran,et al.  Predicting Ebola Severity: A Clinical Prioritization Score for Ebola Virus Disease , 2017, PLoS neglected tropical diseases.

[36]  Judith Breuer,et al.  Clinical and biological insights from viral genome sequencing , 2017, Nature Reviews Microbiology.

[37]  Justin Stoler,et al.  Febrile illness diagnostics and the malaria-industrial complex: a socio-environmental perspective , 2016, BMC Infectious Diseases.

[38]  J. Adeniji,et al.  Non-polio enteroviruses in faeces of children diagnosed with acute flaccid 1 paralysis in Nigeria , 2016 .

[39]  Pardis C Sabeti,et al.  Unbiased Deep Sequencing of RNA Viruses from Clinical Samples , 2016, Journal of visualized experiments : JoVE.

[40]  K. Methawasin,et al.  Transverse Myelitis in Acute Hepatitis A Infection: The Rare Co-Occurrence of Hepatology and Neurology , 2016, Case Reports in Gastroenterology.

[41]  Arndt von Haeseler,et al.  W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis , 2016, Nucleic Acids Res..

[42]  Adeyemi Abayomi Awofala,et al.  HIV epidemiology in Nigeria , 2016, Saudi journal of biological sciences.

[43]  J. Crump,et al.  Estimating the Burden of Febrile Illnesses , 2015, PLoS neglected tropical diseases.

[44]  J. Crump,et al.  Community prevalence of fever and relationship with malaria among infants and children in low-resource areas. , 2015, The American journal of tropical medicine and hygiene.

[45]  S. Günther,et al.  International External Quality Assessment Study for Molecular Detection of Lassa Virus , 2015, PLoS neglected tropical diseases.

[46]  Xiao Yang,et al.  Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa , 2015, PLoS neglected tropical diseases.

[47]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[48]  R. T. Sasmono,et al.  Performance of Simplexa Dengue Molecular Assay Compared to Conventional and SYBR Green RT-PCR for Detection of Dengue Infection in Indonesia , 2014, PloS one.

[49]  J. Simpore,et al.  Screening of Hepatitis G and Epstein-Barr Viruses Among Voluntary non Remunerated Blood Donors (VNRBD) in Burkina Faso, West Africa , 2013, Mediterranean journal of hematology and infectious diseases.

[50]  Minh Anh Nguyen,et al.  Ultrafast Approximation for Phylogenetic Bootstrap , 2013, Molecular biology and evolution.

[51]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[52]  Pardis C Sabeti,et al.  Emerging Disease or Diagnosis? , 2012, Science.

[53]  N. Slevin,et al.  What Three Wise Men have to say about diagnosis , 2011, BMJ : British Medical Journal.

[54]  K. Kang,et al.  Encephalitis Associated with Acute Hepatitis A , 2011, Journal of epilepsy research.

[55]  B. Bonning The Dicistroviridae: An emerging family of invertebrate viruses , 2009, Virologica Sinica.

[56]  Oumar Faye,et al.  One-step RT-PCR for detection of Zika virus. , 2008, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

[57]  Kate E. Jones,et al.  Global trends in emerging infectious diseases , 2008, Nature.

[58]  Curtis A Suttle,et al.  Metagenomic Analysis of Coastal RNA Virus Communities , 2006, Science.

[59]  I. Damon,et al.  Detection of monkeypox virus with real-time PCR assays , 2006, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

[60]  K. Danso,et al.  GB virus C and HIV-1 RNA load in single virus and co-infected West African individuals , 2006, AIDS.

[61]  O. Koroglu,et al.  Hepatitis A virus infection presenting with seizures. , 2005, The Pediatric infectious disease journal.

[62]  S. Falkow Molecular Koch's postulates applied to bacterial pathogenicity — a personal recollection 15 years later , 2004, Nature Reviews Microbiology.

[63]  D. A. Kenny,et al.  The moderator-mediator variable distinction in social psychological research: conceptual, strategic, and statistical considerations. , 1986, Journal of personality and social psychology.