San Francisco 49ers

Shaping up: Aaron Lynch has made strides since dubious start

How does someone pull both hamstrings at the same time?

While running down the field to cover a kickoff, 49ers outside linebacker Aaron Lynch said Tuesday. And by being badly out of shape when doing so.

Lynch, a fifth-round pick out of South Florida in May, didn’t dance around the issue of his conditioning when he arrived in Santa Clara in the spring. Neither did defensive coordinator Vic Fangio, who held Lynch, 21, out of the team’s Aug. 7 preseason opener because he didn’t think the rookie was physically ready.

“He’s a guy that came in here after the draft out of shape, was rounding into shape toward the end of the offseason workouts, then pulled – strangely – both hamstrings at once,” Fangio said Tuesday. “So he spent June and July rehabbing, not training.”

Fangio’s comments added background to the surprisingly critical comment the South Florida strength coach made on Twitter shortly after the draft.

“Thought an organization with 5 Super Bowl titles would have a stricter draft criteria,” Hans Straub wrote of the 49ers. “Clearly, integrity & character are not a priority.”

Straub was suspended, then resigned soon after posting the tweet.

Lynch may not have been a workout warrior in the past, and character concerns caused at last one team to remove him from its draft board in May.

But by all accounts, he’s been a good pupil since joining the 49ers.

Said Fangio: “What little I know about his past, he’s been more diligent than he’s ever been.”

Lynch’s selection came after a series of bad-news stories involving Chris Culliver and Aldon Smith, and coach Jim Harbaugh and general manager Trent Baalke took a risk in drafting him.

Perhaps that’s why Harbaugh said on KNBR on Tuesday that Lynch “was kind of a personal favorite of mine.”

“I just like him,” Harbaugh said. “He’s in the process of learning how to become a pro football player, and I’m proud to report he’s doing a very good job ... eye-popping at times. He’d be thinking small if he just settled for making the team. I think he can be a real fine football player.”

After playing only on special teams against the Ravens and having a limited role against the Broncos, Lynch played 32 snaps against the Chargers on Sunday, more than any of the team’s other outside linebackers. And, like Harbaugh said, he stood out.

The tall, long-armed linebacker batted away two passes, finished with three tackles and had his first sack, which came despite being put in a virtual choke hold by the San Diego right tackle.

“He had some good plays even when they weren’t the type of plays that end up on the stat sheet,” Fangio said. “You know, playing the run, etc.”

Lynch plays the same position as Smith, who is expected to be suspended at the start of the season because of legal issues stemming from a September DUI arrest and weapons charges. The NFL has not said when the suspension will be announced, and Fangio and team officials said they don’t know the timing or how many games Smith could miss.

When Smith missed five games while in an alcohol rehabilitation center last season, Dan Skuta filled in on base downs and Corey Lemonier played passing downs. Fangio said there was a “good chance” that could be the solution this year, too.

In any event, he said the team is better off this year than last.

“Because you have a feeling something may happen at this point of the season, everyone’s getting reps now,” Fangio said. “All the guys that may play for him – Skuta, Lemonier, Lynch, (Chase) Thomas – have been getting a lot of reps, so they’re all ready to go. It’s more of an issue when it happens in the middle of a season and it’s just thrown on you, like it happened last year and then there’s no time to adjust.”

Lynch said he’s trying hard to stay focused, and he’s intent on winning the trust of the veterans on the team.

“Being a pro, you have to have good habits,” he said. “You can’t go out there in practice and be lazy. And that’s what I’ve really caught onto watching the older guys, how Justin Smith, Patrick Willis, Aldon, Ahmad (Brooks), Ray (McDonald) – they all work hard during practice. Nobody takes a day off, really.”

Et cetera – Fangio said the competition to replace injured linebacker NaVorro Bowman will continue into Thursday’s preseason finale in Houston. Michael Wilhoite has started every game during the preseason, but third-round draft pick Chris Borland has shown promise too.

• Brooks was not in uniform for Tuesday’s practice, and instead worked with a trainer, raising the possibility that he won’t play Thursday.

• Safety Antoine Bethea was out of his blue, “no-contact” jersey, signaling that he had passed the league’s post-concussion protocol. Bethea suffered a concussion Aug. 17.