New Jersey Gov. Chris Christie and former Virginia Gov. Bob McDonnell stormed the national stage in 2009 as symbols of the GOP’s anti-Obama momentum, but with both now under federal investigation, Republicans’ unity is shattered and strategists and fellow officeholders struggle to contain the damage.

Mr. McDonnell was indicted Tuesday, while Mr. Christie is facing a state investigation over “Bridgegate” and a federal probe over New Jersey’s use of Superstorm Sandy emergency response money — money that the governor badgered Congress to give him.

Each were political stars and were reportedly on the short list to be the 2012 vice presidential nominee and potential 2016 presidential candidates. Now, strategists are debating whether they are viable at all.

“Both men were seen as possible presidential candidates, so this is a bigger hit for the GOP establishment,” said Keith Appell, a GOP strategist. “Christie is their guy, whereas conservatives have plenty of other horses they can ride besides McDonnell.”

Steve Scheffler, Republican national committeeman from Iowa, said Mr. McDonnell is “probably dead politically — especially in terms of a presidential bid,” but said Mr. Christie may have some life in him, though his problems run deeper than the investigations.

“I wouldn’t declare Christie’s candidacy dead,” Mr. Scheffler said, adding that the biggest obstacle standing in front of Mr. Christie’s presidential aspirations in Iowa is winning over the conservative voters who are at odds with the Republican’s support of in-state tuition for illegal immigrants and his reluctance to trumpet social issues in a more aggressive manner. “I do think he would have trouble making much traction in Iowa.”

Just as fascinating has been how party leaders have handled the two.

While Mr. McDonnell, who left office this month, has been isolated, a few major figures are strenuously defending Mr. Christie, including former Mississippi Gov. Haley Barbour and former New York Mayor Rudolph W. Giuliani.

Mr. Barbour has praised Mr. Christie’s response to the George Washington Bridge scandal and lashed out at the “liberal media elite” for treating the story as if it were on the same level as the Lincoln assassination.

“Haley is one of his most vociferous defenders because Chris Christie has dealt with this crises in the best possible way,” said Bobbie Kilberg, a top GOP fundraiser. “Christie has been forthright. He has been honest. He has been direct and he has taken decisive action.”

He said Mr. Barbour would have done the same in such a situation.

But opposition is also growing — including from former Virginia Attorney General Kenneth T. Cuccinelli II, who told CNN on Tuesday that Mr. Christie should step down as chairman of the Republican Governors Association. Mr. Cuccinelli, who just lost his bid to succeed Mr. McDonnell as Virginia governor, said it will be tough for GOP gubernatorial candidates to run if Mr. Christie is the face of their national party organization.

Others disagree, saying Mr. Christie must stay on the job because he is the only governor who can raise the money necessary to give Republicans their best chance this year of defending and adding to the 29 governorships they control.

High-profile Republicans have remained silent as more details and accusations emerge in New Jersey.

“I think it is the culture of politics these days that when someone is accused of something that the first instinct of all politicians is self-preservation and they run for cover,” said Steve Duprey, a Republican national committeeman from New Hampshire. “They become like turtles and there is not a lot of upside of going out on point for someone else. The old school loyalty is sort of a thing of the past.”

Mr. Duprey, who ran Sen. John McCain’s 2008 presidential campaign in New Hampshire, said the looming 2016 campaign may have something to do with the muted defense of Mr. Christie, as surrogates choose sides.

“If you are a friend of Gov. Scott Walker, for instance, you don’t want to do anything that promotes Gov. Christie over Walker,” Mr. Duprey said.

Mr. McDonnell and his wife, Maureen, were indicted Tuesday on charges that they accepted more than $135,000 in gifts — including private jet trips, vacations and loans — from a businessman.

Mr. McDonnell said he showed poor judgment but did not break the law and will fight the charges.

Mr. Christie, meanwhile, easily won a second term in the November election, but the honeymoon ended this month when emails seemed to indicate that members of Mr. Christie’s inner circle and some of his appointees at the Port Authority of New York and New Jersey were involved in engineering traffic jams on the George Washington Bridge in apparent retaliation for a Democratic mayor’s refusal to endorse the Republican governor’s re-election bid.

The federal government also launched a probe into Superstorm Sandy relief funds that were used to pay for tourism commercials starring Mr. Christie and his family during his re-election push, and a Hoboken mayor claims that the Christie administration threatened to withhold relief funds until the city supported a development project.

Mr. Christie has denied any wrongdoing on his part.

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