COVID: the answer is in the sewage; and another scary mathematical model

Yet another article from Jon Pincus.  i suspect he spends more time scanning the obscure COVID-19 literature than i do reviewing his inspirational findings....

this one was in Nature and suggested that testing sewage for coronavirus may be a useful way to assess the scale of an outbreak and even be an early warning sign of an impending outbreak (see https://www.nature.com/articles/d41586-020-00973-x)

Details:

-- it turns out that more than a dozen research groups are looking at wastewater coronavirus levels as a means to estimate the total number of infections in a community

    -- prior microbial outbreaks (norovirus, antibiotic-resistant bacteria, poliovirus and measles) have been detected by monitoring sewage

-- sewage monitoring may be a very useful approach because coronavirus tends to have high viral loads early on, and in many patients prior to significant symptoms. And therefore prior to many individuals having Covid 19 tests done, as in the"resource-poor" US (at least for Covid-19 testing)

    -- see http://gmodestmedblogs.blogspot.com/2020/04/covid-presenting-as-mild-flu.html for an LA study finding that 5% of patients presenting with mild flu symptoms had COVID

-- wastewater monitoring of  SARS-CoV-2 at Schiphol Airport in Tilburg was able to detect the virus only 4 days after the first case of Covid-19 was found in the Netherlands

-- by following coronavirus levels in wastewater over time, researchers may be able to foresee an increase in infections prior to their becoming clinically evident

    -- one benefit is that an uptick in wastewater levels might be a very concrete incentive to the community to really improve nonmedical public health initiatives such as social distancing, handwashing, using masks and gloves, etc. This may become even more important as the current pandemic continues for months and people may fatigue from continuing their social isolation (ie, the public health effects of targeted interventions for those communities clearly at higher risk may work better than blanket recommendations for all, where some people may feel that they are lower risk than perhaps they actually are and not protect themselves)

    -- and, as a side note here, there might be huge benefit if we find medications that really improve clinical outcomes when given very early in the disease: early detection/treatment in the asymptomatic/prodromal phase might dramatically decrease subsequent ICU admissions

-- coronavirus is detected in feces early on, also prior to significant clinical infection with SARS-CoV-2

    -- http://gmodestmedblogs.blogspot.com/2020/03/covid-19-update-31120.html highlights a study showing that stool samples were positive by day 3 and maxed by day 6-7, and the virus can persistent in stools for up to 13 days after pharyngeal samples are negative (see http://gmodestmedblogs.blogspot.com/2020/04/covid-presistence-of-virus-in.html ) 

-- clearly there are a lot of variables in this wastewater approach, including cutpoints of what are significant changes; and concentrations of the virus in the wastewater will depend on lots of factors (e.g. the concentration of virus in wastewater excrement may be very different in a community where people flush their toilets preferentially for feces, vs a community where lots of uncontamined water ends up in the wastewater)

    -- however, it is likely that if wastewater were tracked over time for individual communities, changes in the SARS-CoV-2 concentration may be really significant...

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As a related issue: the NY Times today reported on a mathematical modeling study suggesting that even a single reported case of Covid-19 has a 51% likelihood of a sustained outbreak in that community, and that 72% of all counties in the US (94% of the population) are likely to have epidemics: see the NY Times article at https://www.nytimes.com/interactive/2020/04/03/us/coronavirus-county-epidemics.html?referringSource=articleShare , and the study: https://cid.utexas.edu/sites/default/files/cid/files/covid-risk-maps_counties_4.3.2020.pdf?m=1585958755 . more details:

    --they used a mathematical tool they developed for the spread of Zika, also often a silent disease, in 2016

    --given the dismally low rates of testing in the US, they assumed that only 10% of cases are reported. other assumptions

        -- an epidemc is >500 cases, and minimum incidence of 10 cases/day

        --the R₀ is 1.5, which is lower than some estimates (this is the effective reproduction number/average number of new cases from one infected individual). though of course their sensitivity analyses positing higher R₀ leads to much worse scenarios

    --based on this model, the chance of an undetected outbreak in counties, by number of reported cases:

        --ZERO: 9%

        --1 case: 51%

        --2 cases: 70%

        --3 cases: 79%

        --10 cases: 95%

        --20 cases : 99% 

        --43 or more cases: 100%

    --their map (figure 1) is a pretty shocking depiction of the probability of outbreaks in the 3142 counties in the US

    --in Texas (whence the study originated), 56% of the countries with 97% of the population has a >50% chance on ongoing Covid-19 transmission

--they suggest proactive social distancing even before 2 cases are reported

    

So, 

--pretty interesting caca (to try to be polite)…. testing wastewater may be an important use of resources to predict subsequent increases in severe Covid-19 cases. And, that can lead to important and expeditious public health measures necessary to stifle the spread of the virus. 

--And the mathematical modeling study really reinforces that even a few known cases likely represents pretty widespread infection in the community and impending local epidemics.

geoff​

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