More than 90 residents and 10 staff members at San Francisco’s largest homeless shelter have tested positive for coronavirus, in a development that homeless advocates say was both predictable and preventable amid massive policy failures.

The outbreak at the MSC South shelter is believed to be the largest reported outbreak in a single shelter in the country. The spike caused a single 12% surge in positive cases in the city, illustrating the magnitude of the crisis in a region that so far has weathered the coronavirus storm well.

San Francisco reported 957 confirmed Covid-19 cases on Monday, a number that was “significantly higher” than the 797 reported on Friday, said Dr Grant Colfax, the director of the San Francisco department of public health, “in large part due to the large numbers of testing we did in the homeless community”.

There will be more, Colfax said.

“The population of people experiencing homelessness face many barriers to health and wellness in normal times, and this pandemic will only exploit and amplify those problems,” he said. “Other cities such as Boston, Los Angeles and Seattle are grappling with a large number of cases of Covid-19 among their homeless populations. We expect to see the same.”

A person sits outside the MSC South homeless shelter in San Francisco. Photograph: John G Mabanglo/EPA

But the outbreak at the MSC South shelter follows weeks of warnings from advocates and local lawmakers that the thousands of people living on San Francisco’s streets or in overcrowded shelters could do little to protect themselves from the virus or help prevent its spread, with calls for the mayor, London Breed, to move the city’s more than 8,000 homeless residents into vacant hotel rooms growing louder each day.

“This [outbreak] was totally preventable and totally predictable,” said Chris Herring, a sociology doctoral candidate at UC Berkeley who works with the Coalition on Homelessness.

Before the coronavirus outbreak, MSC South typically housed 340 people a night, with 200 beds for men only in an open-floor set-up on the second floor. Bunk beds stood about two feet apart, with no partitions, and there was just one hallway of bathrooms to share among everyone. “It was definitely ripe for viral spread, in terms of the designs and the density and the amount of people there,” said Herring, who had spent time at MSC South during his research.

This [outbreak] was totally preventable and totally predictable Chris Herring

The line to get into MSC South used to stretch down the street. The majority of the shelter’s beds were for 90-day stays, but the shelter had more drop-in overnight beds than any other in the city. Its drop-in center acted as a triage for all overnight beds, with some individuals getting shuttled to other shelters where a bed was available. “There was a huge amount of crossover between people and staff within these shelters up until two weeks ago,” Herring said.

Dr Allen Cooper, a retired Stanford University medical school professor who volunteered at the MSC South shelter clinic, had written to Breed to warn her about the conditions for viral spread in the city’s shelters even before the coronavirus outbreak.

In January, he saw a case of norovirus rip through not just MSC South, but spread to a nearby shelter as well. “It was tearing through here,” Cooper said. “Given how fast something like that would spread through the shelter, I just thought that coronavirus would go viral.”

To improve social distancing at the shelters, the facilities stopped receiving new residents and the city resolved to move some shelter residents to other new emergency congregate shelters, including the Moscone Center – a large conference center downtown known for its tech gatherings. Breed maintained that providing every single homeless individual in the city with a hotel room was simply impossible.

On 6 April, the city announced the two first positive cases at MSC South. The city had to rethink its plan for new shelters when photos leaked showing the arrangements at Moscone: thin mats on the floor, divided into physically distanced cells by masking tape. The mayor admitted that authorities had moved 19 individuals from MSC South to Moscone Center before realizing that they had contact with the two positive cases.

By the time the first two cases tested positive at the shelter, Breed was moving into hotel rooms only those who had tested positive, had been exposed to the virus or were already in shelters and considered especially vulnerable to the disease – people over the age of 60 or with underlying health conditions.

An activist protests from her vehicle outside Moscone Center, asking Mayor London Breed to house homeless people using vacant hotels. Photograph: Ben Margot/AP

“The focus has been on waiting until after, what do you do after people get sick,” said Kelley Cutler, the human rights organizer for the not-for-profit Coalition on Homelessness. “But we need to do prevention because for a lot of these folks, it’s too late. Once you wait until after, it’s too late.”

A recent study conducted by researchers at three US universities had determined that in this pandemic, homeless people would be two to three times more likely to die and two to four times more likely to be hospitalized than the general population.

Cutler pointed out that Breed had been proactive with so many of her orders with the coronavirus crisis, but when it came to the homeless population, the city’s response was reactive at best.

By 10 April, the number of positive cases at MSC South had risen to 70, and on Monday it had jumped another 21. In addition, the city has been unable to determine exactly how many of the 987 cases and 15 deaths are of homeless residents. In addition to the 92 MSC South residents and one other shelter resident, Colfax noted that 20% of all Covid-related hospitalizations at Zuckerberg San Francisco general hospital, the city’s safety-net medical facility, were of homeless individuals.

“This could have been averted,” said Cooper, the Stanford medical professor. He questioned what occurred in the week that passed between the first two positive cases and the surge. “Why did it take them so long to do the testing and begin segregating the positive cases?” he said.

By the time officials discovered the outbreak, about 100 residents remained at MSC South, Breed said. All have moved into hotel rooms over the weekend.

City health and homeless officials have argued that the uptick in cases, particularly among the unhoused population in congregated settings like shelters, was to be expected.

“Outbreaks like these were bound to happen,” said Colfax, the San Francisco department of public health official. “This is how coronavirus spreads. Our goal is to slow the spread down and mitigate the bad outcomes we see with this virus.”

A man wearing a face mask directs people to food donations in San Francisco. Photograph: Shannon Stapleton/Reuters

Meanwhile, the city has given a number of reasons for why not every homeless person should be housed in a hotel room during the pandemic. “It would not be fiscally prudent,” said Trent Rhorer, the city’s human services agency director. “It has not been easy to provide adequate staff,” Breed said on Monday. Some homeless individuals have “behavioral health issues that make it difficult for them to abide by the rules”, Colfax said.

Herring fears for the individuals who remain in the shelters. Signs posted on shelter doors now tell guests they can only leave the shelter for one hour a day. “Many of these shelters are just a place to sleep,” Herring said. “Many of them do not have a TV room, a common area. “They’re designed as sleeping quarters. And now people are being told they have to stay here 23 hours and if they leave they cannot come back and have to stay out in the streets.”

Although the city’s department of homelessness and supportive housing says shelter evictions will be limited during the pandemic and that the department will extend guests’ stays, Herring doesn’t think the set-up of the shelters will be sustainable for residents to shelter-in-place, conceivably into June.

“There will be more disruptions inside the shelters, people are going to be kicked out, and they’re not going to be let back in,” he said. “Unless the mayor is going to let people into hotels, we’re going to see more and more people on the streets.”