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State's first cases of South Africa COVID-19 variant identified in Alameda, Santa Clara counties

Cases detected through genomic sequencing efforts at Stanford lab

A Stanford Medicine technician in Dr. Benjamin Pinsky's lab sorts through patient samples for the COVID-19 infection. Courtesy Steve Fisch/Stanford Medicine.

California's first confirmed cases of the South African coronavirus variant have been identified in Alameda and Santa Clara counties, health officials announced Wednesday afternoon.

The Stanford Clinical Virology Lab identified two cases, one in each county, as the B.1.351 variant of SARS-CoV-2, the virus that causes COVID-19.

The patients in both cases have recovered. Dr. Sara Cody, Santa Clara County's health officer and director of public health, said the case in her county involved a person who had returned from international travel in mid-January and first experienced symptoms several days later. A traveling partner also got sick but recovered before being tested for the disease; that person, who lives in the same household, is presumed to have had the mutated virus as well.

Health officials are trying to piece together where the person who tested positive might have contracted the disease. The case is complicated by the pattern of travel the pair engaged in.

There is little evidence so far that the case spread beyond the pair. They followed Santa Clara County's 10-day mandatory quarantine after travel of more than 150 miles outside the county and were isolated in their apartment for the entire infectious period, Cody said.

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"This is an important example of how public health measures can help break the chain of transmission and why it is critical that we as a community continue to avoid travel and quarantine upon return," Cody said.

Dr. Nicholas Moss, Alameda County's health officer, said little is yet known about the case in his county other than the identity of the patient. His staff are still investigating how the person contracted the variant and whether the patient came into contact with others.

The two cases were detected through genomic sequencing. Dr. Benjamin Pinsky, medical director of the Stanford Clinical Virology Lab, said the facility has screened 1,708 positive COVID-19 samples in the past three weeks, mainly from patients at Stanford Hospital, its emergency department, Lucile Packard Children's Hospital Stanford and Valley Care, or from patients under preparation for surgeries. Currently, about 4%-5% of the samples they receive are positive for the virus. The lab then screens the positive samples for mutations. When they find them, they run a genomic sequence on some of the samples to identify other potential variants, he said.

As of Wednesday, they've identified the two South African samples. In the past two weeks, they found four samples of the strain that originated in the United Kingdom and two samples of the less-concerning Brazilian P2 strain.

The South African strain and the Brazilian P1 strain — the latter of which has not yet been identified in California — are troubling because they have multiple mutations that could make vaccines and immunity from the currently dominant COVID-19 strain less effective.

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The Brazilian P2 strain has only one of the mutations, so it is less concerning, according to Pinsky. (Cody said Wednesday that this Brazilian P2 strain has not been found in Santa Clara County.)

Viruses work in different ways to attach to human cells. The virus linked to COVID-19 interacts with cells by way of so-called "spike" genes. The interaction is a factor in the transmissibility of the virus. It can also affect many antibodies the body makes to fight the virus. The South African strain has many mutations in the spike genes, which could impact the efficacy of the vaccines.

Studies have found that the Johnson & Johnson and Novavax COVID-19 vaccines have a 60% efficacy against the South African variant, Pinsky said. Earlier this week, AstraZeneca also put its South African study on hold because its vaccine showed less-than-ideal effectiveness against the strain, he said.

Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, said on Monday that the U.K. variant is becoming widespread and will be the dominant strain in the U.S. by the end of March. The Moderna and Pfizer-BioNTech vaccines are at least 94% effective against the U.K. variant, but are "less so" against the variant from South Africa, he said.

Pfizer's vaccine showed a slightly lower level of efficacy against the South African variant, according to a study by New York University scientists. The company said in late January that other studies show the reduction is unlikely to lead to a significant impact in the effectiveness of the vaccine.

Moderna announced in late January that its vaccine holds up against the U.K. and South African variants. Out of an abundance of caution, it is developing a booster.

Moss, Alameda County's health officer, said that even though the vaccines are less effective against variants, early evidence shows they will continue to provide protection for some time. Still, he and Cody are concerned that more variants might exist undetected. Genomic sequencing must ramp up in order to stay ahead of the ever-evolving virus, they said.

Currently only a fraction of COVID-19 positive cases are sequenced, according to Cody. The county and its partners are actively working to increase sequencing efforts, but there are hurdles.

"It reminds me of the early days of testing," she said, when there wasn't a unified strategy and it took a long time to gear up testing and contact tracing.

"One year ago we were very uncomfortable. … With genomic sequencing, it's a similar story," she said.

So far, there's no standardized genomic sequencing nationwide. California is trying to build a standardized approach across the state, she said.

"The capacity just isn't what it needs to be in order to identify the variants rapidly," she said.

Santa Clara County is in a better place than some other areas, perhaps because there are many academic laboratories with equipment and skills to do the sequencing, she said. Pinsky, for example, said his lab currently runs about 100 genomic sequencing tests per week and it plans to do more.

Moss and Cody stressed that the variants make it all the more important to continue in earnest social distancing, mask wearing and other activities to protect against spreading the virus.

"The more chances the virus has to spread, the more opportunities it has to adapt and create new variants. This is a warning to all of us that we must stay on top of community transmission," Moss said.

Cody added: "We're still in a pretty big pickle, and that's the truth."

The Centers for Disease Control and Prevention on Wednesday released data showing that double masking, such as wearing a cloth face covering on top of a surgical mask, is more effective at reducing virus transmission. For recommendations on double-masking and making sure face coverings are tight-fitting, visit cdc.gov.

Find comprehensive coverage on the Midpeninsula's response to the new coronavirus by Palo Alto Online, the Mountain View Voice and the Almanac here.

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State's first cases of South Africa COVID-19 variant identified in Alameda, Santa Clara counties

Cases detected through genomic sequencing efforts at Stanford lab

by / Palo Alto Weekly

Uploaded: Thu, Feb 11, 2021, 11:12 am

California's first confirmed cases of the South African coronavirus variant have been identified in Alameda and Santa Clara counties, health officials announced Wednesday afternoon.

The Stanford Clinical Virology Lab identified two cases, one in each county, as the B.1.351 variant of SARS-CoV-2, the virus that causes COVID-19.

The patients in both cases have recovered. Dr. Sara Cody, Santa Clara County's health officer and director of public health, said the case in her county involved a person who had returned from international travel in mid-January and first experienced symptoms several days later. A traveling partner also got sick but recovered before being tested for the disease; that person, who lives in the same household, is presumed to have had the mutated virus as well.

Health officials are trying to piece together where the person who tested positive might have contracted the disease. The case is complicated by the pattern of travel the pair engaged in.

There is little evidence so far that the case spread beyond the pair. They followed Santa Clara County's 10-day mandatory quarantine after travel of more than 150 miles outside the county and were isolated in their apartment for the entire infectious period, Cody said.

"This is an important example of how public health measures can help break the chain of transmission and why it is critical that we as a community continue to avoid travel and quarantine upon return," Cody said.

Dr. Nicholas Moss, Alameda County's health officer, said little is yet known about the case in his county other than the identity of the patient. His staff are still investigating how the person contracted the variant and whether the patient came into contact with others.

The two cases were detected through genomic sequencing. Dr. Benjamin Pinsky, medical director of the Stanford Clinical Virology Lab, said the facility has screened 1,708 positive COVID-19 samples in the past three weeks, mainly from patients at Stanford Hospital, its emergency department, Lucile Packard Children's Hospital Stanford and Valley Care, or from patients under preparation for surgeries. Currently, about 4%-5% of the samples they receive are positive for the virus. The lab then screens the positive samples for mutations. When they find them, they run a genomic sequence on some of the samples to identify other potential variants, he said.

As of Wednesday, they've identified the two South African samples. In the past two weeks, they found four samples of the strain that originated in the United Kingdom and two samples of the less-concerning Brazilian P2 strain.

The South African strain and the Brazilian P1 strain — the latter of which has not yet been identified in California — are troubling because they have multiple mutations that could make vaccines and immunity from the currently dominant COVID-19 strain less effective.

The Brazilian P2 strain has only one of the mutations, so it is less concerning, according to Pinsky. (Cody said Wednesday that this Brazilian P2 strain has not been found in Santa Clara County.)

Viruses work in different ways to attach to human cells. The virus linked to COVID-19 interacts with cells by way of so-called "spike" genes. The interaction is a factor in the transmissibility of the virus. It can also affect many antibodies the body makes to fight the virus. The South African strain has many mutations in the spike genes, which could impact the efficacy of the vaccines.

Studies have found that the Johnson & Johnson and Novavax COVID-19 vaccines have a 60% efficacy against the South African variant, Pinsky said. Earlier this week, AstraZeneca also put its South African study on hold because its vaccine showed less-than-ideal effectiveness against the strain, he said.

Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, said on Monday that the U.K. variant is becoming widespread and will be the dominant strain in the U.S. by the end of March. The Moderna and Pfizer-BioNTech vaccines are at least 94% effective against the U.K. variant, but are "less so" against the variant from South Africa, he said.

Pfizer's vaccine showed a slightly lower level of efficacy against the South African variant, according to a study by New York University scientists. The company said in late January that other studies show the reduction is unlikely to lead to a significant impact in the effectiveness of the vaccine.

Moderna announced in late January that its vaccine holds up against the U.K. and South African variants. Out of an abundance of caution, it is developing a booster.

Moss, Alameda County's health officer, said that even though the vaccines are less effective against variants, early evidence shows they will continue to provide protection for some time. Still, he and Cody are concerned that more variants might exist undetected. Genomic sequencing must ramp up in order to stay ahead of the ever-evolving virus, they said.

Currently only a fraction of COVID-19 positive cases are sequenced, according to Cody. The county and its partners are actively working to increase sequencing efforts, but there are hurdles.

"It reminds me of the early days of testing," she said, when there wasn't a unified strategy and it took a long time to gear up testing and contact tracing.

"One year ago we were very uncomfortable. … With genomic sequencing, it's a similar story," she said.

So far, there's no standardized genomic sequencing nationwide. California is trying to build a standardized approach across the state, she said.

"The capacity just isn't what it needs to be in order to identify the variants rapidly," she said.

Santa Clara County is in a better place than some other areas, perhaps because there are many academic laboratories with equipment and skills to do the sequencing, she said. Pinsky, for example, said his lab currently runs about 100 genomic sequencing tests per week and it plans to do more.

Moss and Cody stressed that the variants make it all the more important to continue in earnest social distancing, mask wearing and other activities to protect against spreading the virus.

"The more chances the virus has to spread, the more opportunities it has to adapt and create new variants. This is a warning to all of us that we must stay on top of community transmission," Moss said.

Cody added: "We're still in a pretty big pickle, and that's the truth."

The Centers for Disease Control and Prevention on Wednesday released data showing that double masking, such as wearing a cloth face covering on top of a surgical mask, is more effective at reducing virus transmission. For recommendations on double-masking and making sure face coverings are tight-fitting, visit cdc.gov.

Find comprehensive coverage on the Midpeninsula's response to the new coronavirus by Palo Alto Online, the Mountain View Voice and the Almanac here.

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