Califf was touted as a veteran presence when he was taken in the re-entry draft in December. New Toronto FC president Kevin Payne said at the time that the franchise expected Califf "to provide important leadership as we change the culture of our team."
"We're thrilled to have him on our team," Payne added in the statement.
But after starting the first four games of the season, Califf has been reduced to being a spectator of late, arguably Toronto's fifth choice at centre back.
On Tuesday, he was nowhere to be seen.
"He had a virus last week. He's been away for a few days actually," said Nelsen when asked about the absence.
It's worth noting that Califf was acquired before Nelsen, a former central defender himself who is just two years older than Califf, was installed as manager. Nelsen reminded reporters of the fact when asked if the relationship between club and player was no longer viable.
"When I came in, knowing that Toronto had signed Danny, it was like all five centre backs we've got, it was all for them to compete for two jobs," he said. "Everybody in their career has to go from pecking order one to pecking order five. That's life, it's how you react to it.
"All we want from Danny, all we ask of him is we set up an environment that people can work hard, put their head down and try and get on the spot. That's all we ask of our players."
Asked if there was a future for Califf in a Toronto FC shirt, Nelsen replied: "Of course, everybody here has a future. But it's about putting in an effort, day in and day out, on and off the field."
Going into this season, Califf had played in 207 MLS games over 10 seasons for the Los Angeles Galaxy, Philadelphia Union and Chivas USA. He has also played in Denmark for Aalborg and Midtjylland.
Califf was first-choice at centre-back along with Darren O'Dea for the first four games of Toronto's season. While not fleet of foot, he seemed to have done the job asked.
He missed the next game, against FC Dallas, because of stomach flu. And then it all went south.
Califf was healthy for the trip to Philadelphia the following week, with his California-based family set to see the game. The first ever captain of the Union, Califf has fond memories of his time in Philadelphia.
Nelsen elected to stick with 21-year-old Gale Agbossoumonde, who had made his MLS debut in place of Califf the week before, and Califf found himself on the bench. He did not see action that day and has not stepped on the field in a league game since.
Toronto has used Steven Caldwell and Doneil Henry at centre back recently, with O'Dea shifted to left back. Agbossoumonde has been on the bench.
Califf has made no waves publicly, although it was obvious the Philadelphia snub hurt when he lost his starting job. Toronto hosts the Union in a return match Saturday.
Califf, said to be ailing, was not part of the Toronto match squad in New England last weekend. He was an unused substitute for the five previous league games.
He did play in both semifinal legs of the Amway Canadian Championship against Montreal, winning 2-0 at home and losing 6-0 in Montreal.