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

Abstract

New Zealand, Australia, Iceland, and Taiwan all saw success at controlling their first waves of COVID-19. As islands, they make excellent case studies for exploring the effects of international travel and human movement on the spread of COVID-19. We employed a range of robust phylodynamic methods and genome subsampling strategies to infer the epidemiological history of SARS-CoV-2 in these four countries. We compared these results to transmission clusters identified by the New Zealand Ministry of Health by contract tracing strategies. We estimated the effective reproduction number of COVID-19 as 1–1.4 during early stages of the pandemic, and show that it declined below 1 as human movement was restricted. We also showed that this disease was introduced many times into each country, and that introductions slowed down markedly following the reduction of international travel in mid March 2020. Finally, we confirmed that New Zealand transmission clusters identified via standard health surveillance strategies largely agree with those defined by genomic data. We have demonstrated how the use of genomic data and computational biology methods can assist health officials in characterising the epidemiology of viral epidemics, and for contact tracing.

Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand

“…Our tree is the maximum-clade credibility tree summarizing a posterior distribution of trees inferred by BEAST 2 (14). Genomic sites were partitioned into the 3 codon positions, plus noncoding, as described (3) For each partition, we modeled evolution with an HKY (Hasegawa-Kishino-Yano) substitution model with log-normal(μ = 1, σ = 1.25) prior on κ, frequencies estimated with Dirichlet (1,1,1,1) prior, and relative substitution rates with Dirichlet (1,1,1,1). We used a strict clock model with log-normal(μ = −7, σ = 1.25) prior on mean clock rate, and for the tree prior we used a Bayesian skyline model (15) with Markov chain distribution on population sizes and log-normal(μ = 0, σ = 2) on the first population size.…”

“…Viral genomic sequencing has played a crucial role in tracing and delineating all community outbreaks in New Zealand (3,9,10), complementing border controls, the alert level system, and contact tracing. There has been an effort to sequence the virus from every case-patient.…”

Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area

“…We do not hold information on the duration and specific location of individuals, but a continuum estimate of population mixing that aligns well with the concept of a compartmental ODE model. Mobility and the reduction thereof have been suggested as a proxy to evaluate the reduction of the spread of SARS-CoV-2 ( Douglas et al. 2020 ; Rader et al.…”

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

“…Thus, this slowdown effect is not unique to Switzerland in summer. Importantly, ( 4 ) showed - using genome sequence data - that New Zealand contact tracing was highly effective in identifying SARS-CoV-2 infection clusters. Then, ( 25 ) recently exploited an accidental, partial breakdown of English contact tracing to show that normal contact tracing in early fall 2020 reduced transmissions by 63% in the 6 weeks following a positive case.…”