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Preliminary analysis of SARS-CoV-2 importation & establishment of UK transmission lineages
8th June 2020
Fig8_import-pie-11800×900 104 KB
A limitation of this preliminary analysis is that our estimates do not capture all the statistical uncertainty involved. The analytical framework used here is newly developed and it will take time before we can incorporate all sources of uncertainty in a statistically rigorous manner. The estimates reported here are preliminary and we focus on reporting results that we believe are robust. We have undertaken sensitivity analyses for several parameters and have compared our estimates of SARS-CoV-2 prevalence with those from more sophisticated model-based approaches. We are undertaking further work to explore the sensitivity of our results to the different ways in which UK-specific subtrees (lineages) are identified within the global SARS-CoV-2 phylogeny. Our estimates of the number of infectious individuals in each country are naïve and could be improved. For example, we assume that the probability of a traveller from country X being infectious is the same as that of a member of the general population of country X on the same day. This may be unrealistic when prevalence and rate of inbound travel vary among regions in a country. Our estimates of international rail passenger numbers are more uncertain than those for air and sea travel. The EII represents the varying likelihood of the introduction of infections into the UK but does not model the probability that an infectious arrival will initiate a local transmission lineage. Further work is needed to understand what factors might affect this probability of establishment. We intend to explore further how the number and size of UK transmission lineages observed in our sample relates to the actual number and size of transmission lineages in the general population.
virological.org
8th June 2020
Fig8_import-pie-11800×900 104 KB
Limitations
A limitation of this preliminary analysis is that our estimates do not capture all the statistical uncertainty involved. The analytical framework used here is newly developed and it will take time before we can incorporate all sources of uncertainty in a statistically rigorous manner. The estimates reported here are preliminary and we focus on reporting results that we believe are robust. We have undertaken sensitivity analyses for several parameters and have compared our estimates of SARS-CoV-2 prevalence with those from more sophisticated model-based approaches. We are undertaking further work to explore the sensitivity of our results to the different ways in which UK-specific subtrees (lineages) are identified within the global SARS-CoV-2 phylogeny. Our estimates of the number of infectious individuals in each country are naïve and could be improved. For example, we assume that the probability of a traveller from country X being infectious is the same as that of a member of the general population of country X on the same day. This may be unrealistic when prevalence and rate of inbound travel vary among regions in a country. Our estimates of international rail passenger numbers are more uncertain than those for air and sea travel. The EII represents the varying likelihood of the introduction of infections into the UK but does not model the probability that an infectious arrival will initiate a local transmission lineage. Further work is needed to understand what factors might affect this probability of establishment. We intend to explore further how the number and size of UK transmission lineages observed in our sample relates to the actual number and size of transmission lineages in the general population.
Preliminary analysis of SARS-CoV-2 importation & establishment of UK transmission lineages
This work has been significantly updated and released as a preprint: https://www.medrxiv.org/content/10.1101/2020.10.23.20218446v1 Preliminary analysis of SARS-CoV-2 importation & establishment of UK transmission lineages 8th June 2020 Oliver Pybus1 & Andrew Rambaut2 with Louis du Plessis1...
virological.org