New study finds that closing the toilet lid when flushing isn't all that effective for cutting down viral contamination

Couple things. The first is that this test was on viruses, not bacteria. Prior studies have shown that closing the lid does reduce the amount of cross contamination of fecal matter inoculated with c. difficile. This earlier study’s conclusion was to discourage lidless toilets in hospital settings to reduce the transmission. Which of course went nowhere because lids on public toilets are prohibited by code.

However, that study was of bacteria in chunks of fecal matter getting a free ride in water droplets. This newer study was on a substitute for MS2 bacteriophage, which are much smaller than bacteria, and survive in an aerosol (much smaller than water droplets generated by spray.)

The other is that US toilets were never designed to contain the plume. They were designed long before people thought of such things, and current US building codes mandate the old designs because they provide appropriate ventilation required to make the plumbing work (a sealed lid could affect the flushing such that the bowl water would not stay trapped in the P, opening a path for sewer gases to escape.)
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