TY - JOUR AU - Geoghegan, Jemma AU - Douglas, Jordan AU - Ren, Xiaoyun AU - Storey, Matthew AU - Hadfield, James AU - Silander, Olin AU - Freed, Nikki AU - Jelley, Lauren AU - Jefferies, Sarah AU - Sherwood, Jillian AU - Paine, Shevaun AU - Huang, Sue AU - Sporle, Andrew AU - Baker, Michael AU - Murdoch, David AU - Drummond, Alexei AU - Welch, David AU - Simpson, Colin AU - French, Nigel AU - Holmes, Edward AU - de Ligt, Joep T1 - Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand T2 - Emerging Infectious Disease journal PY - 2021 VL - 27 IS - 5 SP - 1317 SN - 1080-6059 AB - Real-time genomic sequencing has played a major role in tracking the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), contributing greatly to disease mitigation strategies. In August 2020, after having eliminated the virus, New Zealand experienced a second outbreak. During that outbreak, New Zealand used genomic sequencing in a primary role, leading to a second elimination of the virus. We generated genomes from 78% of the laboratory-confirmed samples of SARS-CoV-2 from the second outbreak and compared them with the available global genomic data. Genomic sequencing rapidly identified that virus causing the second outbreak in New Zealand belonged to a single cluster, thus resulting from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data. Access to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks. KW - 2019 novel coronavirus disease KW - coronavirus disease KW - COVID-19 KW - severe acute respiratory syndrome coronavirus 2 KW - SARS-CoV-2 KW - viruses KW - respiratory infections KW - zoonoses KW - genomics KW - infectious disease KW - New Zealand DO - 10.3201/eid2705.204579 UR - https://wwwnc.cdc.gov/eid/article/27/5/20-4579_article ER - End of Reference