I have been going through my bibliography to add the word pandemic where appropriate, and I thought people might be interested in a few works I found that map pretty directly on current concerns, with the earliest example from 1990.
The earliest ones I've identified are closely related: Jack Londons, "The Scarlet Plague" and George Stewart's Earth Abides but still working on it.
2009 Smith, Peter Andrew. “Thirteen.” Neo-Opsis Science Fiction Magazine, no. 17 (2009): 20-26. PSt
Dystopia of a world in which human physical contact has disappeared from fear of disease. Canadian author.
2009 Valentine, Genevieve (b. 1981). “Is This Your Day To Join the Revolution?” Futurismic (2009). http://futurismic.com/2009/09/01/new-fiction-is-this-your-day-to-join-the-revolution-by-genevieve-valentine/. Accessed April 21, 2011. Rpt. in Brave New Worlds. Ed. John Joseph Adams (San Francisco, CA: Night Shade Books, 2011), 267-74; 2nd ed. as Brave New Worlds: Dystopian Stories. Ed. John Joseph Adams (San Francisco, CA: Night Shade Books, 2012), 267-74. PSt
Dystopia in which people are controlled through a fake scare about a disease. Female author.
1999 Baker, Kage [Kate Genevieve] (1952-2010). “Smart Alec.” Asimov’s Science Fiction 23.9 (284) (September 1999): 50-68. Rpt. in Isaac Asimov’s Utopias. Ed. Gardner [Raymond] Dozois and Sheila Williams (New York: Ace Books, 2000), 169-201 with a note on 169. CU-Riv, Merril, PSt
A dystopia in which all the health and social worries of the late 20th century have been enforced and become social practice. Children do not play together for fear of disease. Only licensed adults are allowed to hug a child. Only healthy foods are allowed. Continued in her “Monster Story.” Asimov’s Science Fiction 25.6 (305) (June 2001): 54-69. Female author.
1990 Bergstrom, Elaine. “Net Songs.” The Women Who Walk Through Fire: Women’s Fantasy and Science Fiction Vol. 2. Ed. Susanna J. Sturgis (Freedom, CA: The Crossing Press, 1990), 93-110. PSt US
Right wing dystopia controlling human relationships through the fear of disease. Female author.