In the Talmud (Chulin 10a), Chazal taught that one should not drink water, wine or milk from containers that were left uncovered because a snake and its venom might have gotten into the drink and it will cause the person danger. Today, snakes are not commonly found and the Matei Yehonoson 116:1 says there is a heter to drink from uncovered vessels if no snakes are around, adding that one may be lenient because at the time of the halacha it was only made in a place where snakes were common. Nevertheless, I know people who continue to be stringent on this practice, even covering their water glass between sips. While I understand that poskim are stringent with regard to water left out overnight (see, e.g., Kitzur Shulchan Aruch 33:5), why should anyone need to be stringent during the course of a meal, when a snake would not likely crawl into a water goblet on a Shabbos table without notice?
Rivevos Ephraim Chelek 5:11 writes that in defer Halichos V'Hanahagos(Rav Eliyashiv) was makpid to cover drinks.He brings a story were he covered his drink when he left the room for a second even with someone else there.He also brings a story which happened on Purim where he left room then came back and said don't drink the wine because it was left uncovered .see it inside.