Learning transmission dynamics modelling of COVID-19 using comomodels

This is the author accepted manuscript. The final version is available on open access from Elsevier via the DOI in this recordThe COVID-19 epidemic continues to rage in many parts of the world. In the UK alone, an array of mathematical models have played a prominent role in guiding policymaking. Whilst considerable pedagogical material exists for understanding the basics of transmission dynamics modelling, there is a substantial gap between the relatively simple models used for exposition of the theory and those used in practice to model the transmission dynamics of COVID-19. Understanding these models requires considerable prerequisite knowledge and presents challenges to those new to the field of epidemiological modelling. In this paper, we introduce an open-source R package, comomodels, which can be used to understand the complexities of modelling the transmission dynamics of COVID-19 through a series of differential equation models. Alongside the base package, we describe a host of learning resources, including detailed tutorials and an interactive web-based interface allowing dynamic investigation of the model properties. We then use comomodels to illustrate three key lessons in the transmission of COVID-19 within R Markdown vignette

Assessing the spread of the novel coronavirus in the absence of mass testing

This note outlines a simple method for estimating the spread of the COVID 19 virus in the absence of data on test results for a large, random sample of the population. It applies the method to the UK, and other countries, and finds that to match data on daily new cases of the virus, the estimated model favours high values for the number of people infected but asymptomatic. That result is very sensitive to whether the transmission rate of the virus is di erent for symptomatic and asymptomatic cases, something about which there is significant uncertainty. This illustrates how di icult it is to estimate the spread of the virus until very large samples of the population can be tested

Origins of multi-decadal variability in sudden stratospheric warmings

Sudden stratospheric warmings (SSWs) are major disruptions of the Northern Hemisphere (NH) stratospheric polar vortex and occur on average approximately six times per decade in observation-based records. However, within these records, intervals of significantly higher and lower SSW rates are observed, suggesting the possibility of low-frequency variations in event occurrence. A better understanding of factors that influence this decadal variability may help to improve predictability of NH midlatitude surface climate, through stratosphere–troposphere coupling. In this work, multi-decadal variability of SSW events is examined in a 1000-year pre-industrial simulation of a coupled global climate model. Using a wavelet spectral decomposition method, we show that hiatus events (intervals of a decade or more with no SSWs) and consecutive SSW events (extended intervals with at least one SSW in each year) vary on multi-decadal timescales of periods between 60 and 90 years. Signals on these timescales are present for approximately 450 years of the simulation. We investigate the possible source of these long-term signals and find that the direct impact of variability in tropical sea surface temperatures, as well as the associated Aleutian Low, can account for only a small portion of the SSW variability. Instead, the major influence on long-term SSW variability is associated with long-term variability in amplitude of the stratospheric quasi-biennial oscillation (QBO). The QBO influence is consistent with the well-known Holton–Tan relationship, with SSW hiatus intervals associated with extended periods of particularly strong, deep QBO westerly phases. The results support recent studies that have highlighted the role of vertical coherence in the QBO when considering coupling between the QBO, the polar vortex and tropospheric circulation

Origins of multi-decadal variability in sudden stratospheric warmings

Sudden stratospheric warmings (SSWs) are major disruptions of the Northern Hemisphere (NH) stratospheric polar vortex and occur on average approximately six times per decade in observation-based records. However, within these records, intervals of significantly higher and lower SSW rates are observed, suggesting the possibility of low-frequency variations in event occurrence. A better understanding of factors that influence this decadal variability may help to improve predictability of NH midlatitude surface climate, through stratosphere–troposphere coupling. In this work, multi-decadal variability of SSW events is examined in a 1000-year pre-industrial simulation of a coupled global climate model. Using a wavelet spectral decomposition method, we show that hiatus events (intervals of a decade or more with no SSWs) and consecutive SSW events (extended intervals with at least one SSW in each year) vary on multi-decadal timescales of periods between 60 and 90 years. Signals on these timescales are present for approximately 450 years of the simulation. We investigate the possible source of these long-term signals and find that the direct impact of variability in tropical sea surface temperatures, as well as the associated Aleutian Low, can account for only a small portion of the SSW variability. Instead, the major influence on long-term SSW variability is associated with long-term variability in amplitude of the stratospheric quasi-biennial oscillation (QBO). The QBO influence is consistent with the well-known Holton–Tan relationship, with SSW hiatus intervals associated with extended periods of particularly strong, deep QBO westerly phases. The results support recent studies that have highlighted the role of vertical coherence in the QBO when considering coupling between the QBO, the polar vortex and tropospheric circulation.</p

Interactions between the stratospheric polar vortex and Atlantic circulation on seasonal to multi-decadal timescales

Variations in the strength of the Northern Hemisphere winter polar stratospheric vortex can influence surface variability in the Atlantic sector. Disruptions of the vortex, known as sudden stratospheric warmings (SSWs), are associated with an equatorward shift and deceleration of the North Atlantic jet stream, negative phases of the North Atlantic Oscillation, and cold snaps over Eurasia and North America. Despite clear influences at the surface on sub-seasonal timescales, how stratospheric vortex variability interacts with ocean circulation on decadal to multi-decadal timescales is less well understood. In this study, we use a 1000 year preindustrial control simulation of the UK Earth System Model to study such interactions, using a wavelet analysis technique to examine non-stationary periodic signals in the vortex and ocean. We find that intervals which exhibit persistent anomalous vortex behaviour lead to oscillatory responses in the Atlantic Meridional Overturning Circulation (AMOC). The origin of these responses appears to be highly non-stationary, with spectral power in vortex variability at periods of 30 and 50 years. In contrast, AMOC variations on longer timescales (near 90-year periods) are found to lead to a vortex response through a pathway involving the equatorial Pacific and quasi-biennial oscillation. Using the relationship between persistent vortex behaviour and the AMOC response established in the model, we use regression analysis to estimate the potential contribution of the 8-year SSW hiatus interval in the 1990s to the recent negative trend in AMOC observations. The result suggests that approximately 30 % of the trend may have been caused by the SSW hiatus