A cursory review of the drug's use at VA hospitals earlier this year found no positive effects on COVID-19 patients. Though the review indicated a possible connection between hydroxychloroquine and higher mortality rates, the paper was inconclusive and not a peer-reviewed scientific study.
Wilkie pointed to the lack of peer review and said the paper's calling the drug's efficacy and safety as a coronavirus treatment into question were not clinical studies. He added that hydroxychloroquine was prescribed by doctors in consultation with families, often for patients who were out of options.
"Many of those studies that you refer to don't look at the underlying medical conditions. In our VA, when we use this we use it with veterans who are -- in many cases -- in the last hours of life, but we also use them under FDA regimen."
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The FDA has temporarily approved the use of hydroxychloroquine -- usually prescribed for malaria, lupus and certain types of arthritis -- allowing doctors to use the drug on some COVID-19 patients. The agency urges "close patient supervision" because side effects include deadly heart rhythm problems. Clinical trials of the drug's effectiveness as a coronavirus treatment are ongoing and remain inconclusive.
Wilkie said that the VA is not currently administering the drug much, estimating 130 cases in May, out of about 1,650 active patients. But he vowed the VA will continue offering it to coronavirus patients who have no other hope.
"It might help, and as long as there's a 'might' in there, we're going to do everything we can to try," he said.
ABC News' Anne Flaherty and Quinn Owen contributed to this report.