Real-time digital pathogen surveillance - the time is now

Genome Biology

Volumn 16, Issue 1, 2015, Pages

  Gardy, Jennifer ^a   Loman, Nicholas J ^b   Rambaut, Andrew ^c  

^a BRITISH COLUMBIA CENTRE FOR DISEASE CONTROL   (Canada)

^b UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Ebola; Real time whole genome sequencing; Salmonella; Surveillance

Indexed keywords

BIOSURVEILLANCE; EBOLAVIRUS; ESCHERICHIA COLI; GENE SEQUENCE; GENETIC EPIDEMIOLOGY; GENETIC LINE; HIGH THROUGHPUT SEQUENCING; HUMAN; INFLUENZA VIRUS A H1N1; NONHUMAN; NOTE; PANDEMIC INFLUENZA; SALMONELLA ENTERICA; VIRUS GENOME; VIRUS TRANSMISSION; ANIMAL; DISEASE OUTBREAKS; GENOMICS; GENOTYPING TECHNIQUE; HEALTH SURVEY; MOLECULAR EPIDEMIOLOGY; PROCEDURES; PUBLIC HEALTH; ZOONOSES;

SALMONELLA;

ANIMALS; DISEASE OUTBREAKS; GENOMICS; GENOTYPING TECHNIQUES; HUMANS; MOLECULAR EPIDEMIOLOGY; POPULATION SURVEILLANCE; PUBLIC HEALTH; ZOONOSES;

EID: 84937955824     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-015-0726-x     Document Type: Note

References (13)

1. Marí Saéz A, Weiss S, Nowak K, Lapeyre V, Zimmermann F, Düx A, et al. Investigating the zoonotic origin of the West African Ebola epidemic. EMBO Mol Med. 2015;7:17-23.
2. WHO Ebola Situation Report 1st July 2015. http://apps.who.int/ebola/current-situation/ebola-situation-report-1-July-2015 .
3. Reusken CBEM, Haagmans BL, Müller MA, Gutierrez C, Godeke G-J, Meyer B, et al. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study. Lancet Infect Dis. 2013;13:859-66.
4. Atlas of Salmonella. http://www.cdc.gov/salmonella/reportspubs/salmonella-atlas/ .
5. Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, et al. Pandemic potential of a strain of influenza A (H1N1): early findings. Science. 2009;324:1557-61.
6. Quick J, Ashton P, Calus S, Chatt C, Gossain S, Hawker J, et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 2015;16:114.
7. Greninger AL, Naccache SN, Federman S, Yu G, Mbala P, Bres V, et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. bioRxiv 2015. 10.1101/020420 .
8. EHEC Outbreak Crowdsourcing Github Wiki. https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki .
9. Neher RA, Bedford T. nextflu: Real-time tracking of seasonal influenza virus evolution in humans. Bioinformatics. 2015;pii:btv381.
10. Microreact. http://microreact.org/ .
11. Update on Ebola virus circulating in Sierra Leone and Guinea. http://virological.org/t/updateon-ebola-virus-circulating-in-sierra-leone-and-guinea/151 .
12. Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, et al. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med. 2011;365:718-24.
13. Schatz MC, Phillippy AM. The rise of a digital immune system. Gigascience. 2012;1:4.