I grew up in backwoods Baptist churches in Ontario, and communion always meant passing around plates of tiny cubes of bread and tiny cups of grape juice to share the memory of our sacrificed Savior. It wasn’t until I was a teenager that I learned, to the shock of my sanitation sensibilities, that in some churches everyone drinks from the same cup during communion. “Is that really sanitary?” I asked a friend who went to such a church. I was firmly assured that the alcohol content of the wine they used was sure to sterilize the cup, and the transmission of germs was absolutely minimal. Of course, alcohol kills germs, and that answer seemed perfectly satisfactory at the time. In the years since then I have become part of a tradition where many members do share a common cup (though there are also tiny cups available), and have gained enough microbiology know-how to ask the same question more thoroughly. Just how sanitary is the sharing of a common cup? The answer depends on two main factors: How good is wine at killing germs, and what sort of germs we’re dealing with.
How Good is Ethanol at Killing Germs?
Ethanol has been a popular active ingredient in hand sanitizers for years now and there’s plenty of data to show that it’s highly effective. One of the main ways ethanol affects germs is by bending their proteins out of shape . All living things rely on having a collection of functional proteins that are carefully assembled and folded into their correct shapes to do their various jobs and keep cells alive. Unfortunately for life, there are plenty of ways to get proteins bent out of shape. Many proteins rely on being surrounded by water to be held in their correct shape, and being surrounded by a significantly different substance, like ethanol, squishes the proteins into unusual shapes that simply don’t work. The worst thing is that many can’t be bent back into shape so they have to be rebuilt from scratch. In the mean-time, the bacteria or virus might be too broken to continue living or being dangerous, which we hope is the case when using hand sanitizer.
However, in order for any disinfectant to be effective it needs both enough concentration and enough contact time. An effective disinfectant like hand sanitizer will have a concentration of between 60-90% ethanol by volume and be effective within 30 seconds . Unfortunately, wines tend to have an ethanol content of only 12-14% unless they have been fortified . That’s pretty bad news for any hope of effective disinfection because even a solution of 20% ethanol has been found to take between 5-24 hours to kill some bacteria, and 10% ethanol can take days . The good news is that there are other factors about wine, such as its acidity, that can work together with the ethanol to kill some types of bacteria in just 15-45 minutes . So wine can be a pretty fast disinfectant, but perhaps not fast enough to prevent you from sharing your salivation as well as salvation with those behind you in the communion line.
What Kind of Germs are We Dealing With?
Bacteria and viruses are extraordinarily diverse, and many types just aren’t of concern in this discussion (unless you suspect your pew-mates of something like gargling with raw pork before church). The good news is that most types of bacteria probably won’t be of concern at all because of the relatively large numbers that most pathogenic bacteria need to cause you serious illness. The few bacteria that are aggressive enough to be dangerous from ingesting a few hundred or less of them (e.g. Shigella  come from sources you wouldn’t expect in a church, like feces. They also don’t tend to be spread orally, so bacteria are probably just not a serious concern here.
On the other hand, viruses do tend to be spread orally. Cold, Flu, and cold-sore viruses (Rhinovirus, Influenza virus, and Herpes Simplex Virus 1, respectively) are all reasonable infection risks in any situation where large numbers of the public are touching their mouths to the same surface. 60-80% ethanol solutions are highly effective at inactivating all of these viruses, but the effectiveness of ethanol decreases significantly at concentrations below 50% . It’s difficult to tell just how ineffective wine is at inactivating these viruses without tests being done specifically on these viruses with wine. However, it does seem reasonable to cautious here because at very least we know that wine is a lot worse at disinfecting surfaces than something like hand sanitizer.
So, Good News?
So it does seem reasonably possible that a common cup could share the common cold, or a cold sore. For someone who has an infection, it’s definitely most considerate to others in public to avoid potentially spreading germs in this way, but that’s just perennial good advice. Most bacteria are probably not a risk at all. Additionally, churches often employ other precautions, like wiping the cup between users, which can help keep surfaces cleaner. The poor disinfectant quality of wine likely makes virus transmission more of a concern than most people realize, but with proper care taken by sick people, I wouldn’t start ringing any alarm bells about the potential of a church-based flu epidemic without more positive evidence on the topic of wine inactivating viruses.
As for me, I’m happy sticking with the tiny cups for now. More for my tradition’s sake than sanitation.
 Rutala WA, Weber DJ, [HICPAC]Healthcare Infection Control Practices Advisory Committee. 2008. Guideline for infection and sterilization in healthcare facilities, 2008. Atlanta (GA): Centres for Disease Control and Prevention; [updated 2009 Dec 29; cited 2016 Jan 9]. Available from: http://www.cdc.gov/hicpac/Disinfection_Sterilization/6_0disinfection.html
 Robinson J, Harding J, editors. 2015. The Oxford companion to wine. [internet]. Oxford (UK): Oxford University Press; [cited 2016 Jan 9]. Available from: https://books.google.ca/books?id=8yegCgAAQBAJ&pg=PA1&source=gbs_toc_r&cad=3#v=onepage&q&f=false
 Dietzie W. 1936. Disinfectant action of wine. British Medical Journal 1(3920): 372-373. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2122476/?page=1
 Shigella spp. Pathogen Safety Data Sheet [internet]. 2011. Ottawa (ON): Public Health Agency of Canada; [cited 2016 Jan 9]. Available from: http://www.phac-aspc.gc.ca/lab-bio/res/psds-ftss/shigella-eng.php