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Sat Jun 20, 2020, 08:57 AM

Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period

The paper to which I'll refer is this one: Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. (Stephen M. Kissler1*, Christine Tedijanto2*, Edward Goldstein2, Yonatan H. Grad1†‡, Marc Lipsitch, Science Vol. 368, Issue 6493, pp. 860-868 May 22, 2020)

The paper is about a month old. I didn't get around to checking it out until this morning. I'm logged in, but it should be open sourced as all Covid papers are. It's an interesting study of the possible long term behavior of the virus should vaccination efforts fail.

Since it's probably open sourced, there's no need for me to discuss much of it, so I'll just offer some excerpts and post a few pictures at which interested persons can look.

From the introductory text:

The ongoing severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) pandemic has caused nearly 500,000 detected cases of coronavirus disease 2019 (COVID-19) illness and claimed >20,000 lives worldwide as of 26 March 2020 (1). Experience from China, Italy, and the United States demonstrates that COVID-19 can overwhelm even the healthcare capacities of well-resourced nations (2–4). With no pharmaceutical treatments available, interventions have focused on contact tracing, quarantine, and social distancing. The required intensity, duration, and urgency of these responses will depend both on how the initial pandemic wave unfolds and on the subsequent transmission dynamics of SARS-CoV-2. During this initial pandemic wave, many countries have adopted social distancing measures and some, like China, are gradually lifting them after achieving adequate control of transmission. However, to mitigate the possibility of resurgences of infection, prolonged or intermittent periods of social distancing may be required. After the initial pandemic wave, SARS-CoV-2 might follow its closest genetic relative, SARS-CoV-1, and be eradicated by intensive public health measures after causing a brief but intense pandemic (5). Increasingly, public health authorities consider this scenario unlikely (6). Alternatively, the transmission of SARS-CoV-2 could resemble that of pandemic influenza by circulating seasonally after causing an initial global wave of infection (7)...

...The pandemic and postpandemic transmission dynamics of SARS-CoV-2 will depend on factors including the degree of seasonal variation in transmission, the duration of immunity, and the degree of cross-immunity between SARS-CoV-2 and other coronaviruses, as well as the intensity and timing of control measures. SARS-CoV-2 belongs to the Betacoronavirus genus, which includes the SARS-CoV-1 coronavirus, the Middle East respiratory syndrome (MERS) coronavirus, and two other HCoVs, HCoV-OC43 and HCoV-HKU1. The SARS-CoV-1 and MERS coronaviruses cause severe illness with approximate case fatality rates of 9 and 36%, respectively, but the transmission of both has remained limited (9). HCoV-OC43 and HCoV-HKU1 infections may be asymptomatic or associated with mild to moderate upper respiratory tract illness; these HCoVs are considered the second most common cause of the common cold (9)...


The authors model SARS-COV-2 by studying closely related viruses with which there is long experience.



The caption:

Fig. 1 Effects of depletion of susceptibles and seasonality on Re by strain and season.
Shown are the estimated multiplicative effects of HCoV-HKU1 incidence (red), HCoV-OC43 incidence (blue), and seasonal forcing (gold) on weekly Res of HCoV-HKU1 (top) and HCoV-OC43 (bottom), with 95% confidence intervals. The black dot (with 95% confidence interval) plotted at the start of each season is the estimated coefficient for that strain and season compared with the 2014–2015 HCoV-HKU1 season. The seasonal forcing spline is set to 1 at the first week of the season (no intercept). On the x-axis, the first “week in season” corresponds to epidemiological week 40.




The caption:

Fig. 2 Transmission model fits for HCoV-OC43 and HCoV-HKU1.
(A) Weekly percent positive laboratory tests multiplied by percent ILI for HCoV-OC43 (blue) and HCoV-HKU1 (red) in the United States between 5 July 2014 and 29 June 2019 (solid lines) with simulated output from the best-fit SEIRS transmission model (dashed lines). (B and C) Weekly Re values estimated using the Wallinga–Teunis method (points) and simulated Re from the best-fit SEIRS transmission model (line) for HCoV-OC43 and HCoV-HKU1. The opacity of each point is determined by the relative percent ILI multiplied by percent positive laboratory tests in that week relative to the maximum percent ILI multiplied by percent positive laboratory tests for that strain across the study period, which reflects uncertainty in the Re estimate; estimates are more certain (darker points) in weeks with higher incidence.


The authors consider several possible scenarios based on the (still unknown) long term dynamics of infection:

We summarized the postpandemic SARS-CoV-2 dynamics into the categories of annual outbreaks, biennial outbreaks, sporadic outbreaks, or virtual elimination (tables S2 to S7). Overall, shorter durations of immunity and smaller degrees of cross-immunity from the other betacoronaviruses were associated with greater total incidence of infection by SARS-CoV-2, and autumn establishments and smaller seasonal fluctuations in transmissibility were associated with larger pandemic peak sizes. Model simulations demonstrated the following key points...

...SARS-CoV-2 can proliferate at any time of year...

...If immunity to SARS-CoV-2 is not permanent, it will likely enter into regular circulation...

...High seasonal variation in transmission leads to smaller peak incidence during the initial pandemic wave but larger recurrent wintertime outbreaks...

...If immunity to SARS-CoV-2 is permanent, the virus could disappear for 5 or more years after causing a major outbreak...

...Low levels of cross-immunity from the other betacoronaviruses against SARS-CoV-2 could make SARS-CoV-2 appear to die out, only to resurge after a few years...


Here's a graphic from one scenario:



The caption:

Fig. 6 Intermittent social distancing scenarios with current and expanded critical care capacity.
SARS-Cov-2 prevalence (black curves) and critical cases (red curves) under intermittent social distancing (shaded blue regions) without seasonal forcing (A and C) and with seasonal forcing (B and D). Distancing yields a 60% reduction in R0. Critical care capacity is depicted by the solid horizontal black bars, and the on/off thresholds for social distancing are depicted by the dashed horizontal lines. (A) and (B) are the scenarios with current critical care capacity in the United States and (C) and (D) are the scenarios with double the current critical care capacity. The maximal wintertime R0 is 2.2 and for the seasonal scenarios the summertime R0 is 1.3 (40% decline). Prevalence is in black and critical care cases are in red. To the right of each main plot (E to H), the proportion immune over time is depicted in green with the herd immunity threshold (horizontal black bar).


There is also scenarios involving herd immunity, etc... For more graphics and information, one should check out the full paper.

Our Republican fellow citizens, those most invested in a cult of personality and hatred, will be working this weekend to advance herd immunity. It appears that some are from out of town in Tulsa, the city with the worst history of post slavery racist violence, for which it was clearly chosen by the racist Steven Miller, the racist "brain" of the brainless administration. Of course, it will kill a lot of innocent people, but that has not troubled Republicans ever going back to 1968 and the "Southern (Race Baiting) Strategy."

Happily however, the worst of them - and among the "worst" are anyone who sets foot in Tulsa to worship the Orange God of Hatred - will have a high probability of doing themselves in, and perhaps their equally stupid friends and family. I have no compassion whatsoever for anyone who includes such people among "friends" and "family."

We do not know, however, the real dynamics or the immunological effects of SARS-CoV-2, and thus, it is quite possible that the Tulsa transmission may further Putin's goal, so expertly realized, of destroying America over the long term.

For the remaining human beings in our country, who have fathers and/or are fathers, I wish you the happiest of Father's days.

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