The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand

Abstract

Background. Real-time genomic sequencing has played a major role in tracking the global spread and local transmission of SARS-CoV-2, contributing greatly to disease mitigation strategies. After effectively eliminating the virus, New Zealand experienced a second outbreak of SARS-CoV-2 in August 2020. During this August outbreak, New Zealand utilised genomic sequencing in a primary role to support its track and trace efforts for the first time, leading to a second successful elimination of the virus. Methods. We generated the genomes of 80% of the laboratory-confirmed samples of SARS-CoV-2 from New Zealand's August 2020 outbreak and compared these genomes to the available global genomic data. Findings. Genomic sequencing was able to rapidly identify that the new COVID-19 cases in New Zealand belonged to a single cluster and hence resulted from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data. Interpretation. Access to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks.

Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations

“…We have demonstrated how the rapid real-time availability and assessment of viral genomic data can complement and augment health surveillance strategies, and thus improve the accuracy of contact tracing methods. As the pandemic has progressed, real-time whole genome sequence data has been integrated into the health response of the four countries discussed here (Geoghegan et al, 2020; Seemann et al, 2020; Gudbjartsson et al, 2020b; Taiwan Centers for Disease Control, 2020b). Genome sequencing is increasingly affordable and shared global surveillance resources such as NextStrain and GISAID are becoming more complete and useful.…”

Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

“…The copyright holder for this this version posted November 11, 2021. ; https://doi.org /10.1101/2021.11.11.21266107 doi: medRxiv preprint on 15 June. We compared our estimates for the transmission damping factor between Switzerland in spring, summer, and fall 2020 with New Zealand before and after an epidemic breakpoint in mid-May 2020 when local transmission was briefly eradicated (9). From this point until early August, all cases in New Zealand were linked to managed quarantine facilities at the border.…”

“…From this point until early August, all cases in New Zealand were linked to managed quarantine facilities at the border. Then, a new community outbreak was identified on 11 August (20). Case numbers were subsequently held at lower levels through December 2020 (Figure 3B).…”

“…This assumption enables estimation of population-level transmission dynamics from pathogen genome data. For example, (8)(9)(10) showed that public health measures reduced SARS-CoV-2 transmission rates in Israel, New Zealand, and Washington State, USA.…”

Compliance with Covid-19 Non-Medicinal Preventive Protocol and Intent to Accept Covid-19 Vaccine Among Adults in South Eastern Nigeria

“…This is particular in Africa where the absence of good health facilities and rising population increase the risk of disease. Coronavirus disease 2019 (COVID- 19) outbreak was rst noticed in Hubei Province, Wuhan, China in 2019 and has spread to virtually all parts of the world. It has so far affected 123 countries in the world, infecting fourteen million six hundred and seventy-four thousand, sis hundred and sixty-six (14,674,666) people and resulting into six hundred and nine thousand, six hundred and eighteen (609,618) deaths worldwide (2) (Worldmeter, 2020).…”