There were two other male Quills living in Virginia City in 1870. In 1880 at least one had died leaving a widow and two small children. It is possible that they are the parents of the child who died in Oct 1879 (mortality schedules are for the year preceding the taking of the census, so a child who died in Oct would have died in 1879, not 1880). What evidence is there that a child named Thomas Brendan existed?
I'm finding it very hard to believe that it took thirty years for anyone to notice there was an extra child floating about. ;-p Charles is probably a nephew. Given both of his parents were born in PA, I'm going to guess he may actually be an Egan. You'd have to do a little digging to try to locate him prior to that census.