How San Francisco led the way in which on COVID-19 analysis

Through a combination of strict lockdown, masking, and evidence of vaccination guidelines, San Francisco managed to keep hospital admissions and deaths from COVID-19 lower than most parts of the country.

But that wasn’t the only thing that made San Francisco stand out during the pandemic. The city is home to a leading medical establishment and some of the world’s foremost infectious disease experts who are at the cutting edge of local and global understanding of the disease.

“San Francisco really is the epicenter of SARS-COV-2 research,” said Dr. Nevan Krogan, director of the Quantitative Biosciences Institute at the University of California, San Francisco. “A lot of people in the Bay Area may not know how much we support this as quarterback.”

With San Francisco and the rest of the world now facing the Omicron variant, local medical leaders say we not only understand a lot more than we did a year ago, but also have more tools to handle the rising cases and the developing variants fight.

In a year when everything stagnated, here are the local discoveries that have moved us forward.

Understand how the mutating virus bypasses our immune response

Much of what we understand about COVID-19 so far revolves around transmission and how individuals can be protected from the virus spreading. But Krogan’s team at the Quantitative Biosciences Institute is charting new frontiers for therapeutics, showing how the coronavirus affects our immune response and mutates once an infection occurs.

The alpha-covid variant – considered the first “questionable variant” – developed mutations that enabled it to suppress the immune system’s early response to infection, according to one this month in Nature by researchers from QBI and University College London published study. Understanding these mutations and how the virus evolves is key not only to tracking future variants, but also to developing new drugs to treat COVID.

“What we found very exciting here is that this new variant suppresses the immune response compared to the older line of the virus,” said Nevan. “After the virus enters our cells, other mutations could contribute to its survival and replication. But nobody talks about the immune response. “

The researchers also observed that similar mutations occur in the Delta and Omicron variants. As breakthrough cases with the Omicron variant continue to grow, Krogan believes the need for better therapeutics is becoming more pressing and hopes the new results can help explain why some people experience COVID-19 symptoms for months have extended.

First detection of Omicron variants in the USA

Just a few weeks after the Omicron variant was first reported in South Africa, the small team of scientists around Dr. UCSF’s David Chiu successfully reported the first known case of the variant in the United States.

The team received a sample at around 6 p.m. on November 30 from an infected traveler who had returned to San Francisco from South Africa. At sunrise, the team had used a tiny device called a nanopore sequencer to generate the genome sequence that confirmed it was an omicron.

“We were able to confirm the detection of Omicron in five hours and had almost the entire genome in eight hours,” said Chiu on December 2nd. “Yesterday evening at 4 o’clock we were able to conclusively prove that it was an infection of the omicron variant.”

Omicron is now the predominant version of the coronavirus in the country and the Bay Area, and its rapid detection has allowed researchers to more quickly understand how it aligns or differs from Delta and other variants.

Vaccination safety for pregnant women

As one of the largest vaccination campaigns in history began across the country that year, questions began to be circulated about the effects of the vaccine on expectant mothers and their babies. After a wave of misinformation about how the vaccine affects fertility, UCSF researchers provided some of the earliest evidence that the messenger RNA vaccine is actually safe for expectant mothers and was not transmitted through breast milk.

The small study analyzed the breast milk of seven women who had each received either a Pfizer or Moderna mRNA vaccine.

“The results reinforce the current recommendations that the mRNA vaccines are safe during breastfeeding and that breastfeeding individuals receiving the COVID vaccine should not stop breastfeeding,” said Dr. Stephanie L. Gaw, Assistant Professor of Maternal-Fetal Medicine at UCSF and author of the study that appeared in JAMA Pediatrics.

New frontiers for COVID neutralizing antibodies

Another blockbuster that year came in April when the QBI Coronavirus Research Group and researchers from the Agency of Science, Technology and Research in Singapore published a study showing varying degrees of effectiveness on various neutralizing antibodies used in COVID-19 therapies will.

The joint study, published in Cell in April, found that various antibodies can inhibit or increase syncytia formation, which occurs in the airway tissue of COVID-infected patients and has been linked to severe tissue damage.

“For vaccine design, we first have to find the right places where antibodies should be developed. The technology for introducing mRNA into an individual … is phenomenal. How do you construct the correct (antibody) substitutions? ”Dr. Charles S. Craik said the results on a virtual panel in September. “It makes it extremely exciting to keep researching how we get this dynamic … but in the end you have to find something that works by making the right antibodies.”

The results are becoming increasingly important now as some early research shows that the tools and therapies that worked well against the Delta variant may not be as effective against Omicron.

sjohnson@sfexaminer.com