Barbie Halaska, necropsy manager with the Marine Mammal Center, cut into a dead juvenile gray whale to take a blubber sample on Limantour Beach at Point Reyes National Seashore in May. Photo: Justin Sullivan/Getty Images

June 29, 2020

For residents of San Francisco, the sight of gray whales making their way into the bay this spring has been a rare treat.

But for local marine scientists, the whale sightings have brought increasing alarm. The coronavirus pandemic is upending their effort to determine why, for the second year in a row, whales have been taking what amounts to a wrong turn into San Francisco Bay.

Something is deeply amiss, either in the animals or in the ocean. Gray whales are long-distance migration champions. Every spring, they leave their breeding grounds in the warm water lagoons of Mexico’s Baja Peninsula for their feeding grounds north of Alaska. In the fall, they make the journey back, a total of 10,000 miles. They don’t typically break for snacks on the way, which is why their appearance in San Francisco Bay, during the middle of their northbound migration, has been so troubling.

Bill Keener, a research associate at the Marine Mammal Center in Sausalito, the largest marine mammal hospital in the world, believes the whales’ visits to the bay hold a clue to solving a larger mystery. Over the first five months of this year alone, 111 gray whales washed ashore along their annual migratory path — far more than the average of 29 deaths per year reported by the National Oceanic and Atmospheric Administration between 2001 and 2018.

In 2019, 215 gray whales died on the same route, 14 of them in the San Francisco Bay Area — seven times the annual average of deaths the previous 18 years. Those deaths prompted NOAA to declare an “unusual mortality event” — which led to emergency funding to the Sausalito center and other research centers to investigate why animals that are near the top of the marine food chain and a key indicator of ocean health would be dying off at such alarming rates.

But the coronavirus has severely constrained the ability of teams to work together to dismantle and analyze the carcasses of these whales. There’s no gas for the boats; social distancing makes collaboration difficult; and, with scientists and graduate student team members sequestering, whale strandings are not sending off the alerts they once did.

Perched on the coast of Sausalito, above the strait where the Pacific Ocean flows into the bay, the Marine Mammal Center is a key link in a network of research stations scattered along the West Coast, from Mexico to Canada. It’s also one of the few U.S. institutions with a large enough staff to regularly perform full whale autopsies, known as necropsies.

A full necropsy offers scientists a rare opportunity to investigate the clues embedded in a dead whale’s stomach, brain, organs, skin and blood, and then draw a conclusion about the cause of death, which is critical to understanding how to keep the species alive.

But necropsies present a daunting logistical challenge. Time is of the essence, and the clock starts ticking as soon as a whale dies somewhere offshore. When a whale dies, in most cases its carcass fills with gases released from the intestine, which causes it to float to the surface. It’s vital to get to the site as quickly as possible.

Depending on water temperature and other factors, there may only be several days before the gases are released and the whale drops to the seabed. The sooner scientists get to the whale, the better the chance of collecting critical samples.

In normal times, the Sausalito center would send up to a dozen scientists to the scene of a whale stranding. Such a large team makes all the difference when trying to quickly dissect a rotting 40- to 50-foot-long carcass weighing up to 90,000 pounds. They examine the skin for parasites and bruising, and then remove it, along with the fat and the blubber, measuring each and taking photographs.

Blood samples are collected to send to serology labs, looking for antibodies to identify whether illness was a factor. Others stand inside the whale’s reeking internal cavities, racing to look at the heart, lungs, brain and intestines before the organs decompose and can no longer offer reliable data. A necropsy with a full team can be completed in three to four hours.

Some of the first clues about mass deaths of gray whales were found off the coast of Mexico, where the whales breed and give birth. At El Vizcaino Biosphere Reserve in Mexico, Steven Swartz, who leads the research there, was one of the first to notice something amiss with gray whales when, in the winter of 2018, he recorded unusually low numbers of calves, increased mortalities and more “skinny” lone whales.

By spring 2019, 14 of those gray whales ended up stranded on beaches in the San Francisco Bay Area and Mendocino County, and the Sausalito center was able to conduct full necropsies on 13 of them. That number of necropsies was record-breaking: In the nine years prior, the center had averaged just six necropsies each year of all whale species.

Frances Gulland, former senior scientist at the Sausalito center who is now a researcher at the U.C. Davis School of Veterinary Medicine, said the whale deaths could be linked to a number of factors, including ship collisions, fishing gear entanglements, parasites or infectious diseases.

Evidence points to another possible culprit: malnutrition because of climate change in the Arctic, the whales’ primary feeding ground. Gray whales follow the food web that forms around the edges of the ice, filtering the sediment on the sea bottom to ingest tiny invertebrates. As the Arctic ice retreats they are traveling farther north in search of nourishment.

Changes in diet could impact whales’ sustenance over the long journey to Mexico and back each year. But there is not enough data, Dr. Gulland said, to conclusively identify whether the speed of Arctic ice disintegration would correlate with the high stresses seen among the whales.

This year’s spike in whale strandings could have provided more definitive evidence about which of these factors was to blame.

But then the coronavirus hit.

Mr. Keener’s work tracking whales was stopped in its tracks. His boat was stuck at the dock in Sausalito, unable to obtain fuel from the marina’s gas station, which was closed to abide by the state’s shelter-in-place order.

The first stranding of the season was reported on March 30, about two weeks after Gov. Gavin Newsom closed down the state. The whale team scrambled. Social-distancing guidelines meant that just five people could fit on one of the Marine Mammal Center’s 12-foot inflatable speedboats.

Dr. Gulland led the procedure that day on Angel Island, in the middle of the bay, with a team half its usual size. It took hours just for the stripped-down crew, masked and gloved, to take off the 440-pound head and roll it on the beach in order to examine the brain.

“Trying to roll something as heavy as a whale head with four people is very difficult,” Dr. Gulland recalled. When they finally rolled it over, too much time had passed and the brain had liquefied.

The liquefaction of a whale’s brain, holder of so many clues about a whale’s life and death, is one of the key factors they’re fighting against as the clock ticks. The process can take a few hours or a few days depending on water and air temperature and size of animal, among other factors.

The partial necropsy Dr. Gulland’s team was able to conduct with such a limited crew provided little more than the sex of the stranded whale, its rough age and any signs of superficial bruising. Since then, NOAA has reported 23 strandings on the coasts of California, Washington, Oregon, and Alaska, and 88 others in Mexican waters. None have undergone a full necropsy.

By mid-June, the moment for investigating whale deaths had passed. Most healthy whales are back in Alaska by now. The mystery of the gray whale deaths will remain unresolved.

“We have climate change in the Arctic,” said Dr. Gulland. “We have animals moving between Mexico, the U.S., Canada. We have Covid. We have big, large decomposing things that are difficult to handle.”

She added: “This is a big ecological mystery, and it’s incredibly difficult to tease out because of all these factors.”