SARS CoV 2 super-spreaders �(and super-spreading Variant of Concern 202012/01)

Marek Kochańczyk, Frederic Grabowski, Grzegorz Preibisch , Stanisław Giziński and Tomasz Lipniacki

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Institute of Fundamental Technological Research,

Polish Academy of Sciences, Warsaw, Poland

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Department of Mathematics, MISMAP

SARS CoV 2 super-spreaders

R₀ – basic reproduction number

• definition: Expected number of secondary cases infected by a single primary case (without any protective measures)
• critical parameter characterizing an outbreak
• actual value matters:

It informs about extent of control measures required to stop pandemic

It determines the immune proportion required to achieve herd immunity: 1 – 1/R₀

Our R₀ estimate based on spring, 2020

wave of pandemic

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Early WHO R₀ estimate, based on epidemic in China

R₀ = 4.7–11.4

R₀ = 1.4–2.5

SEIR model

~ Lauer et al. (2020) medRxiv

SEIR model (variant)

~ Lauer et al. (2020) medRxiv

R₀(T_d)

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Weaver et al.

(2005) PLoS Med.

also: Kochańczyk et al.

(2020) MMNP

R₀

estimation based on the doubling time T_d

Doubling time (T_d)

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• based on cases:

(2 weeks after 100 exceed)

Doubling time (T_d)

• based on deaths:

(2 weeks after 10 exceed)

this study

Kucharski et al.

(2020) Lancet

Wu et al.

(2020) Lancet

R₀ = 4.7–11.4

Reproduction numer estimate based on the doubling time

in contrast to nearly all early estimates…

R₀ of COVID-19, early reports from WHO

“Human-to-human transmission is occurring and a preliminary R₀ estimate of 1.4–2.5 was presented.”

(January 2020)

“The dynamics likely approximated mass action and radiated from Wuhan to other parts of Hubei province and China, which explains a relatively high R₀ of 2–2.5.”

(February 2020)

R₀ of COVID-19, early reports, other

(Boldog et al., February 2020, J. Clin. Med.)

Underestimation of R₀ was caused by� �overestimation of the doubling time (T_d)

(2020) Lancet

(2020) Nat. Med.

(2020) Lancet

(2020) NEJM

τ =

Lack of super-spreading,

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in the early chain of epidemic transmissions,

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caused overestimation of the doubling time (T_d)

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SEIR model stochastic dynamics with super-spreading

SEIR model stochastic simulations:

100 trajectories, hyper-spreaders (:= responsible for ⅔ of infections) ρ = 1%

SEIR model stochastic simulations:

5000 trajectories per histogram

T_d in the presence of super-spreading

T_d

Take-home message:

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If you estimate R₀ at the very beginning of the outbreak,

you will likely underestimate its value.

End of part one�����

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Published in RSOS

Super-spreading Variant of Concern 202012/01

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Spread of A20.EU1 (A222V substitution) and VOC-202012/01 in England,

GISAID data

Variant of Concern 202012/01 mutations:

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also known as B.1.1.7 lineage, first collected on September 20, 2020, in Kent, UK

(GISAID sequence accession number EPI_ISL_601443).

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The lineage, characterized by nine spike protein mutations

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Deletions: 69‐70HV, 145V;

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Substitutions: N501Y, A570D, D614G, P681H, T716I, S982A, D1118H

Replicative advantage of VOC 202012/01 in England,

with respect to A20.EU1, GISAID data

Rt^VOC/Rt^20A.EU1 = 2.17 [95% CI: 1.98–2.37]

for 43–47 week fitting window

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Rt^VOC/Rt^20A.EU1 = 1.85 [95% CI: 1.74–1.97]

For 43-51 week fitting window

Rt^VOC/Rt^20A.EU1 in (1.85 -2.17)

Grabowski et al. Viruses 2021

CONCLUSONS

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The VOC 202012/01 strain had about twofold replicative advantage over the A20.EU1 strain of SARS‐CoV‐2, that was dominating in England in November, 2020.

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The replication numer R₀ of SARS-CoV-2 is increasing due to advantageous mutations.

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Comment: at some point advantageous mutations are those allowing to infected vaccinated or recovered individuals

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Thank You !