Reposted from Dr. Judith Curry’s Climate Etc.

Posted on July 27, 2020 by niclewis

By Nic Lewis

I showed in my May 10th article Why herd immunity to COVID-19 is reached much earlier than thought that inhomogeneity within a population in the susceptibility and in the social-connectivity related infectivity of individuals would reduce, in my view probably very substantially, the herd immunity threshold (HIT), beyond which an epidemic goes into retreat. I opined, based on my modelling, that the HIT probably lay somewhere between 7% and 24%, and that evidence from Stockholm County suggested it was around 17% there, and had been reached. Mounting evidence supports my reasoning.^[1]

I particularly want to highlight an important paper published on July 24th “Herd immunity thresholds estimated from unfolding epidemics” (Aguas et al.).^[2] The author team is much the same as that of the earlier theoretical paper (Gomes et al.^[3]) that prompted my May 10th article.

Aguas et al. used a SEIR compartmental epidemic model modified to allow for inhomogeneity, similar to the model I used although they also considered further variants. They fitted their models to scaled daily new cases data from four European countries for which disaggregated regional case data was also readily available. In all cases they found a better fit from their models incorporating heterogeneity to the standard homogeneous assumption SEIR model. They found that:

Homogeneous models systematically fail to fit the maintenance of low numbers of cases after the relaxation of social distancing measures in many countries and regions.

Aguas et al. estimate the HIT at between 6% and 21% for the countries in their analysis – very much in line with the range I suggested in May. They also found that their HIT estimates were robust to various changes in their model specification. By contrast, if the population were homogeneous or were vaccinated randomly, the estimated HIT would have been around 65% –80%, in line with the classical formula, {1 – 1/R₀}, where R₀ is the epidemic’s basic reproduction number.[4]

Aguas et al.’s Figure 3, reproduced below, shows how the HIT reduces with increasing variation either in susceptibility (given exposure) or in connectivity, which affects both an individual’s susceptibility (via altering exposure to infection) and infectivity. The coloured dots and vertical lines show the inferred position of each of the four countries they analysed in each of these (separately modelled) cases.

Aguas et al. Fig. 3 Herd immunity threshold with gamma-distributed susceptibility (top) or connectivity related exposure to infection (bottom). Curves generated with the SEIR model (Equation 1-4) assuming values of R0 estimated for the study countries assuming gamma-distributed: susceptibility [top]; connectivity (and hence exposure to infection) [bottom]. Herd immunity thresholds (solid curves) are calculated according to the formula 1 − (1/R₀)^{1/(1 + CV^2)} for heterogeneous susceptibility and 1 − (1/R₀)^{1/(1 + 2 CV^2)} for heterogeneous connectivity. Final sizes of the corresponding unmitigated epidemics are also shown (dashed).

As Aguas et al. say in their Abstract:

These findings have profound consequences for the governance of the current pandemic given that some populations may be close to achieving herd immunity despite being under more or less strict social distancing measures.

The underlying reason for the classical formula being inapplicable is, as they say:

More susceptible and more connected individuals have a higher propensity to be infected and thus are likely to become immune earlier. Due to this selective immunization by natural infection, heterogeneous populations require less infections to cross their herd immunity threshold than suggested by models that do not fully account for variation.

The Imperial College COVID-19 model (Ferguson et al.[5]) is a prime example of one that does not adequately account for variation in individual susceptibility and connectivity.

Aguas et al. point out that consideration of heterogeneity in the transmission of respiratory infections has traditionally focused on variation in exposure summarized into age-structured contact matrices. They showed that, besides this approach typically ignoring differences in susceptibility given virus exposure, the aggregation of individuals into age groups leads to much lower variability than that they found from fitting the data. The resulting models appeared to differ only moderately from homogeneous approximations.

A key reason for variability in susceptibility to COVID-19 given exposure to the SARS-CoV-2 virus causing is that the immune systems of a substantial proportion (35% to 80%) of unexposed individuals have T-cells, circulating antibodies or other components that are cross-reactive to SARS-CoV-2 and can be expected to provide substantial resistance to it.[6] [7] [8] [9] Such components likely arise from past exposure to common cold or other coronaviruses, or to influenza.[10] Not being specific to SARS-CoV-2, and typically not being antibodies, such immune system components are not normally detected in seroprevalence or other tests for immunity to SARS-CoV-2.

I will end with a follow up to my June 28th article focusing on Sweden. In it, I concluded that it was likely the HIT had been surpassed in the three largest Swedish regions, and in the country as a whole, by the end of April notwithstanding that COVID-19-specific antibodies had only been detected in 6.3% of the population.[11] I also projected, based on their declining trend, that total COVID-19 deaths would likely only be about 6,400. Subsequent developments support those conclusions. Swedish COVID-19 deaths have continued to decline, notwithstanding a return to more travel and less social distancing, and are now down to 10 to 15 a day. According to the latest Financial Times analysis,[12] excess mortality in Sweden over 2020 to date was 5,500, or 24%. That is only about half the excess mortality percentage for the UK (45%), Italy (44%) and Spain (56%), and is also lower than for France (31%), the Netherlands (27%) and Switzerland (26%), despite Sweden not having imposed a lockdown or shut primary schools. Moreover, total mortality in Sweden over the last 24 months is now lower than over the previous 24 months, despite an upward trend in the old age population.

Nicholas Lewis                                               27 July 2020

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[1] One example, further supporting my superspreader-based evidence of variability in social connectivity, is Miller et al: Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel medRxiv 22 May 2020  https://doi.org/10.1101/2020.05.21.20104521 This paper shows that 1-10% of infected individuals caused 80% of infections. That points to variability in social connectivity related susceptibility and infectivity quite likely being higher than I modelled .

[2] Aguas, R. and co-authors: Herd immunity thresholds estimated from unfolding epidemics” medRxiv 24 July 2020 https://doi.org/10.1101/2020.07.23.20160762

[3] Gomes, M. G. M., et al.: Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold. medRxiv 2 May 2020. https://www.medrxiv.org/content/10.1101/2020.04.27.20081893v1

[4] The basic reproduction number of an epidemic, R₀, measures how many people, on average, each infected individual infects at the start of the epidemic. If R₀ exceeds one, the epidemic will grow, exponentially at first. But, assuming recovered individuals are immune, the pool of susceptible individuals shrinks over time and the current reproduction number falls. The proportion of the population that have been infected at the point where the current reproduction number falls to one is the ‘herd immunity threshold’ (HIT). Beyond that point the epidemic is under control, and shrinks.

[5] Neil M Ferguson et al.: Impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcare demand. Imperial College COVID-19 Response Team Report 9, 16 March 2020, https://spiral.imperial.ac.uk:8443/handle/10044/1/77482

[6] Grifoni, A.et al.: Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals. Cell 11420, 2020 https://doi.org/10.1016/j.cell.2020.05.015

[7] Braun, J., et al.: Presence of SARS-CoV-2 reactive T cells in COVID-19 patients and healthy donors. medRxiv 22 April 2020 https://www.medrxiv.org/content/10.1101/2020.04.17.20061440v1.

[8] Le Bert, N. et al.: Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals. bioRxiv 27 May 2020. https://doi.org/10.1101/2020.05.26.115832

[9] Nelde, A. et al.: SARS-CoV-2 T-cell epitopes define heterologous and COVID-19-induced T-cell recognition. ResearchSquare 16 June 2020.  https://www.researchsquare.com/article/rs-35331/v1

[10] Lee, C., Koohy, H., et al.: CD8+ T cell cross-reactivity against SARS-CoV-2 conferred by other coronavirus strains and influenza virus. bioRxiv 20 May 2020. https://doi.org/10.1101/2020.05.20.107292.

[11] Such seroprevalence is likely to significantly understate the proportion of the population who have had COVID-19, since asymptomatic or mild disease often results in undetectably low antibody levels (Long, Q. X. et al.: Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections. Nat Med. 18 June 2020 https://doi.org/10.1038/s41591-020-0965-6 . Such patients will nevertheless be immune to reinfection (Sekine, K. et al.: Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19. bioRxiv 29 June 2020 https://doi.org/10.1101/2020.06.29.174888).965-6

[12] https://www.ft.com/content/a26fbf7e-48f8-11ea-aeb3-955839e06441. Data updated to 13 July

Originally posted here, where a pdf copy is also available

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