Hundreds to thousands of Atlantic menhaden have been dying in the Thames River, the lower Connecticut River, Clinton harbor and the Quinnipiac River over the past week, prompting the state Department of Energy and Environmental Protection to launch a study of potential causes.

David Simpson, director of the Marine Fisheries Division of DEEP, said Thursday that the probable cause of the fish kill is a virus that causes “whirling” or “spinning” disease that spreads quickly through schools of menhaden, a common forage fish also called bunker.

“They’ve been exhibiting the classic whirling behavior, where they swim in a circular pattern and pivot on their tail,” Simpson said. “They die in three to five days.”

Simpson said he started getting calls from fishermen and boaters over the weekend who noticed dead fish in the water and others swimming in circles.

On Wednesday he collected samples of the dead fish for analysis. In the Thames, the dead fish have been reported in several locations between the Naval Submarine Base in Groton and Norwich harbor.

“I’m still getting calls,” Simpson said.

In Norwich harbor on Thursday, several of the dead fish could be seen floating near the docks and riprap along the shore. Simpson said most of the dead 10- to 14-inch fish are sinking to the bottom rather than floating or washing up on shore.

Mike Valentine, Norwich harbormaster, said he first heard about the fish kill from boaters who noticed dead fish while traveling upriver on the Thames over the weekend.

“A few of them have come in with the tide, and I’ve also seen them doing that whirling thing,” Valentine said.

Mass die-offs are common whenever there is an abundance of menhaden, especially during the summer months when bluefish chase schools into sheltered waters with low levels of dissolved oxygen, Simpson said.

“The tightly packed schools rapidly use up the oxygen in the water and suffocate,” he said.

Since the recent fish kill occurred early in the season before warmer water temperatures lower levels of dissolved oxygen, the virus is the most likely cause, he said. But the investigation is continuing.

Menhaden are an important forage fish for wildlife and also an important commercial fish. About 400 million pounds are harvested annually, mostly in the Chesapeake Bay and New Jersey, and processed into animal feed and fish oil and used as bait for lobster, crab and other fisheries. Simpson said there is also a small commercial and recreational menhaden fishery in Connecticut.

“They’re the most heavily harvested fish on the East Coast,” Simpson said.

In 2013, the Atlantic States Marine Fisheries Commission set quotas on the menhaden fishery to limit the total catch and prevent overfishing. Since then, the population has grown significantly.

“They’re more abundant now than at any time since the 1970s,” Simpson said.

The virus, he said is probably “the collateral effect of high population density.”

The virus is not a threat to human health or other wildlife, he added.

DEEP urges anyone who witnesses a fish kill to contact the Marine Fisheries Division at (860) 434-6043 or by email at deep.marine.fisheries@ct.gov.

j.benson@theday.com

Twitter: @BensonJudy