Rapid in-country sequencing of whole virus genomes to inform

rabies elimination programmes [version 1; peer review: awaiting peer review] Kirstyn Brunker , Gurdeep Jaswant , S.M. Thumbi , Kennedy Lushasi , Ahmed Lugelo , Anna M. Czupryna , Fred Ade , Gati Wambura , Veronicah Chuchu , Rachel Steenson , Chanasa Ngeleja , Criselda Bautista , Daria L. Manalo , Ma. Ricci R. Gomez , Maria Yna Joyce V. Chu , Mary Elizabeth Miranda , Maya Kamat , Kristyna Rysava , Jason Espineda , Eva Angelica V. Silo , Ariane Mae Aringo , Rona P. Bernales , Florencio F. Adonay , Michael J. Tildesley , Denise A. Marston , Daisy L. Jennings , Anthony R. Fooks , Wenlong Zhu , Luke W. Meredith , Sarah C. Hill , Radoslaw Poplawski , Robert J. Gifford , Joshua B. Singer , Mathew Maturi , Athman Mwatondo , Roman Biek , Katie Hampson1,2

[1]  P. Lemey,et al.  Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages — Application to rabies virus spread in Iran , 2019, Molecular ecology.

[2]  A. Ramette,et al.  Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells , 2019, Genes.

[3]  J. Benavides,et al.  An evaluation of Brazil’s surveillance and prophylaxis of canine rabies between 2008 and 2017 , 2019, PLoS neglected tropical diseases.

[4]  David A. Eccles,et al.  Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa , 2019, bioRxiv.

[5]  D. Marston,et al.  Pan-lyssavirus Real Time RT-PCR for Rabies Diagnosis. , 2019, Journal of visualized experiments : JoVE.

[6]  J. Mcgrane,et al.  Lessons for rabies control and elimination programmes: a decade of One Health experience from Bali, Indonesia. , 2019, Revue scientifique et technique.

[7]  E. Schelling,et al.  Reaching for the low hanging fruits: One health benefits of joint crop–livestock services for small-scale farmers , 2019, One health.

[8]  E. Wright,et al.  Bats and Viruses: Emergence of Novel Lyssaviruses and Association of Bats with Viral Zoonoses in the EU , 2019, Tropical medicine and infectious disease.

[9]  B. Bruce,et al.  Zoonotic Source Attribution of Salmonella enterica Serotype Typhimurium Using Genomic Surveillance Data, United States , 2019, Emerging infectious diseases.

[10]  Kyriakos Efthymiadis,et al.  Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples , 2018, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[11]  F. Balloux,et al.  From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic , 2018, Trends in microbiology.

[12]  C. Rupprecht,et al.  Non‐human primates as a reservoir for rabies virus in Brazil , 2018, Zoonoses and public health.

[13]  I. Tiembré,et al.  Bolstering human rabies surveillance in Africa is crucial to eliminating canine-mediated rabies , 2018, PLoS neglected tropical diseases.

[14]  Karthik Gangavarapu,et al.  An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar , 2018, Genome Biology.

[15]  L. Boykin,et al.  Real time portable genome sequencing for global food security , 2018, bioRxiv.

[16]  M. Berriman,et al.  Eradication genomics—lessons for parasite control , 2018, Science.

[17]  T. Peto,et al.  Detection of Viral Pathogens With Multiplex Nanopore MinION Sequencing: Be Careful With Cross-Talk , 2018, bioRxiv.

[18]  U. Obolski,et al.  Genomic and epidemiological monitoring of yellow fever virus transmission potential , 2018, Science.

[19]  Joshua B. Singer,et al.  GLUE: a flexible software system for virus sequence data , 2018, BMC Bioinformatics.

[20]  Adam Kushner,et al.  Electricity and generator availability in LMIC hospitals: improving access to safe surgery. , 2018, The Journal of surgical research.

[21]  P. Lemey,et al.  Landscape attributes governing local transmission of an endemic zoonosis: Rabies virus in domestic dogs , 2018, Molecular Ecology.

[22]  N. Chitnis,et al.  Vaccination of dogs in an African city interrupts rabies transmission and reduces human exposure , 2017, Science Translational Medicine.

[23]  Mauricio O. Carneiro,et al.  Scaling accurate genetic variant discovery to tens of thousands of samples , 2017, bioRxiv.

[24]  Jennifer L. Gardy,et al.  Towards a genomics-informed, real-time, global pathogen surveillance system , 2017, Nature Reviews Genetics.

[25]  Marius Gilbert,et al.  Using Viral Gene Sequences to Compare and Explain the Heterogeneous Spatial Dynamics of Virus Epidemics , 2017, Molecular biology and evolution.

[26]  Tiziana Lembo,et al.  Driving improvements in emerging disease surveillance through locally relevant capacity strengthening , 2017, Science.

[27]  D. Marston,et al.  First Complete Genomic Sequence of a Rabies Virus from the Republic of Tajikistan Obtained Directly from a Flinders Technology Associates Card , 2017, Genome Announcements.

[28]  X. de Lamballerie,et al.  Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host , 2017, Virus evolution.

[29]  L. Real,et al.  Processes Underlying Rabies Virus Incursions across US–Canada Border as Revealed by Whole-Genome Phylogeography , 2017, Emerging infectious diseases.

[30]  J. Crump,et al.  One Health contributions towards more effective and equitable approaches to health in low- and middle-income countries , 2017, Philosophical Transactions of the Royal Society B: Biological Sciences.

[31]  S. F. Aguiar,et al.  Establishment and cryptic transmission of Zika virus in Brazil and the Americas , 2017, Nature.

[32]  Trevor Bedford,et al.  Virus genomes reveal factors that spread and sustained the Ebola epidemic , 2017, Nature.

[33]  M. Shi,et al.  Successful strategies implemented towards the elimination of canine rabies in the Western Hemisphere , 2017, Antiviral research.

[34]  E. Zaikova,et al.  Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer. , 2017, Journal of biomolecular techniques : JBT.

[35]  L. Real,et al.  Application of high-throughput sequencing to whole rabies viral genome characterisation and its use for phylogenetic re-evaluation of a raccoon strain incursion into the province of Ontario. , 2017, Virus research.

[36]  Trevor Bedford,et al.  Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples , 2017, Nature Protocols.

[37]  J. Dushoff,et al.  Surveillance to Establish Elimination of Transmission and Freedom from Dog-mediated Rabies , 2016, bioRxiv.

[38]  Marco Vignuzzi,et al.  Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts , 2016, PLoS pathogens.

[39]  Stephen W. Martin,et al.  2016: the beginning of the end of rabies? , 2016, The Lancet. Global health.

[40]  J. Zinsstag,et al.  Validation of a Rapid Rabies Diagnostic Tool for Field Surveillance in Developing Countries , 2016, PLoS neglected tropical diseases.

[41]  Oliver G. Pybus,et al.  Mobile real-time surveillance of Zika virus in Brazil , 2016, Genome Medicine.

[42]  Christl A. Donnelly,et al.  Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting , 2016, PLoS pathogens.

[43]  Sunny E. Townsend,et al.  Mobile Phones As Surveillance Tools: Implementing and Evaluating a Large-Scale Intersectoral Surveillance System for Rabies in Tanzania , 2016, PLoS medicine.

[44]  S. Cleaveland,et al.  Integrating serological and genetic data to quantify cross-species transmission: brucellosis as a case study , 2016, Parasitology.

[45]  B. Quiambao,et al.  Molecular and mathematical modeling analyses of inter-island transmission of rabies into a previously rabies-free island in the Philippines. , 2016, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[46]  David A. Matthews,et al.  Real-time, portable genome sequencing for Ebola surveillance , 2016, Nature.

[47]  G. Wilkie,et al.  Elucidating the phylodynamics of endemic rabies virus in eastern Africa using whole-genome sequencing , 2015, Virus evolution.

[48]  Joshua Quick,et al.  Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella , 2015, Genome Biology.

[49]  J. Crump,et al.  One health: Endemic zoonoses in the tropics: a public health problem hiding in plain sight , 2018 .

[50]  N. Loman,et al.  A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.

[51]  C. Happi,et al.  Empowering African genomics for infectious disease control , 2014, Genome Biology.

[52]  D. Streicker,et al.  The role of viral evolution in rabies host shifts and emergence , 2014, Current opinion in virology.

[53]  S. Cleaveland,et al.  Implementing Pasteur's vision for rabies elimination , 2014, Science.

[54]  Samuel Soubeyrand,et al.  A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data , 2014, Proceedings of the Royal Society B: Biological Sciences.

[55]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[56]  L. Nel,et al.  Dog rabies in southern Africa: regional surveillance and phylogeographical analyses are an important component of control and elimination strategies , 2013, Virus Genes.

[57]  P. Klepac,et al.  Towards the endgame and beyond: complexities and challenges for the elimination of infectious diseases , 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

[58]  X. de Lamballerie,et al.  Next generation sequencing of viral RNA genomes , 2013, BMC Genomics.

[59]  Akira Noguchi,et al.  Genetic Diversity and Geographic Distribution of Genetically Distinct Rabies Viruses in the Philippines , 2013, PLoS neglected tropical diseases.

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

[61]  David L. Bergman,et al.  Molecular Inferences Suggest Multiple Host Shifts of Rabies Viruses from Bats to Mesocarnivores in Arizona during 2001–2009 , 2012, PLoS pathogens.

[62]  Donald A Henderson,et al.  The eradication of smallpox--an overview of the past, present, and future. , 2011, Vaccine.

[63]  M. Suchard,et al.  Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus , 2010, PLoS pathogens.

[64]  Tiziana Lembo,et al.  Exploring reservoir dynamics: a case study of rabies in the Serengeti ecosystem. , 2008, The Journal of applied ecology.

[65]  C. Packer,et al.  Molecular epidemiology identifies only a single rabies virus variant circulating in complex carnivore communities of the Serengeti , 2007, Proceedings of the Royal Society B: Biological Sciences.

[66]  V. Souza,et al.  Molecular epizootiology of rabies associated with terrestrial carnivores in Mexico. , 2005, Virus research.

[67]  Nipada Ruankaew,et al.  Transmission dynamics of rabies virus in Thailand: Implications for disease control , 2005, BMC infectious diseases.

[68]  C. Rupprecht,et al.  Mongoose rabies in southern Africa: a re-evaluation based on molecular epidemiology. , 2005, Virus research.

[69]  Nevio Zagaria,et al.  Disease eradication, elimination and control: the need for accurate and consistent usage. , 2004, Trends in parasitology.

[70]  S. Cleaveland,et al.  A hundred years of rabies in Kenya and the strategy for eliminating dog-mediated rabies by 2030 [version 2; peer review: 4 approved] , 2020 .

[71]  SallyAnn Harbison,et al.  A review of the potential of the MinION™ single‐molecule sequencing system for forensic applications , 2018, WIREs Forensic Science.

[72]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..