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“It’s a little bit too soon to tell what the impact will be on supply and long term quality over time,” said Lindsey Bolger, who heads up coffee sourcing for Keurig Green Mountain.

Still, the companies are trying to ensure that their future supply isn’t affected, so they are working closely with growers on better practices that will help them avoid contamination.

“Supporting the farmer’s ability to access information, technology and resources allows them to adapt to these uncertainties and ensures the longevity of our industry’s supply chain,” said Craig Russell, Starbucks Global Coffee executive vice president. Starbucks even bought a Costa Rican farm for research purposes.

USAID intends to work with Texas A&M to step up research on rust-resistant coffee varieties and help Latin America better monitor and respond to the fungus. The U.S. already collaborates with some of the coffee companies and other international organizations to finance replanting of different varieties of trees.

The effort is part of the Obama administration’s Feed the Future program, which aims to rid the world of extreme poverty through agricultural development and improved nutrition.

While the effort has helped hungry children around the globe, “we’re at risk of backtracking because of coffee rust,” Shah says.

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Follow Mary Clare Jalonick on Twitter: http://twitter.com/MCJalonick