A strain was a genetic variant or subtype of a microorganism.
In 2366, Paul Stubbs compared the nanite infestation of the USS Enterprise-D's computer core to watching a strain of the Leutscher virus reproduce. (TNG: "Evolution")
In a fantasy created by Barash's neural scanners on Alpha Onias III in 2367, William T. Riker was told he had been infected with a strain of Altarian encephalitis that had supposedly lain dormant within before becoming active sixteen years later. (TNG: "Future Imperfect")
Later that year, Jean-Luc Picard speculated that Beverly Crusher may have had a fast-growth strain of Diomedian scarlet moss to explain its showing one day of growth in less time than had apparently elapsed. (TNG: "Clues")
In 2368, Crusher wondered if a new strain of Iresine Syndrome had developed, to explain the normal histamine count in the comatose Deanna Troi and Riker. (TNG: "Violations")
In 2370, Mora Pol asked Jadzia Dax if an organic strain taken from an infected Odo matched silicate-based lifeforms from L-S VI. (DS9: "The Alternate")
In an imaginary scenario experienced by Kathryn Janeway in 2373, Janeway was informed by The Doctor that she had contracted a virulent form of the Vidiian phage that was spreading rapidly through her system. (VOY: "Coda")
In 2374, The Doctor claimed an injured Romulan's blood contained a strain of the Terothka virus as a ruse to get onto the bridge of the hijacked USS Prometheus. (VOY: "Message in a Bottle")
In 2375, The Doctor informed "DaiMon Torrot" – in fact Seven of Nine, whose own personality had been suppressed by those she’d assimilated while a Borg drone – that "he" had contracted a nasty strain of the Ankaran flu. (VOY: "Infinite Regress")