USA: 233 San Francisco healthcare workers in vaccine breakthough outbreak

At least 233 staff members at two major San Francisco hospitals, most of them fully vaccinated, tested positive for the coronavirus this month.  About 75 to 80 percent of the more than 50 staff members infected at Zuckerberg San Francisco General Hospital were fully vaccinated, Dr. Lukejohn Day, the hospital’s chief medical officer, said in an interview on Saturday. The University of California, San Francisco Medical Center said in a statement issued on Friday that 153 of its 183 infected staff members had been fully vaccinated. report


Finland: 80% vaccine breakthrough in hospital with B16172 Delta #coronavirus variant – PPE no longer effective




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USA: At least 125,000 vaccine breakthrough infections, 1,400 dead

At least 125,000 fully vaccinated Americans have tested positive for Covid and 1,400 of those have died, according to data collected by NBC News.  The total number of breakthrough cases is likely higher than 125,683, since nine states, including Pennsylvania and Missouri, did not provide any information, while 11, like Florida, did not provide death and hospitalization totals. Four states gave death and hospitalization numbers, but not the full tally of cases.

NBC report


WAPO: 35,000 symptomatic Covid-19 infections per week among 162 million vaccinated Americans

USA: 20% vaccine breakthrough rate in California and rising

California has announced that the percentage of vaccine breakthrough infections in fully-vaccinated residents is rising. In June 2021 it was 20%, and has so far doubled every month.

In March 2021, vaccinated people accounted for only 2% of all infections. In April, that rose to 5%. In May, it was 11%.  The rise coincides with the rise of the more transmissible Delta variant in the county, which now accounts for 84% of all variants recently identified

“The Delta variant is a game-changer,” said Los Angeles County Public Health Director Barbara Ferrer said on Thursday. report




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USA: Delta now the dominant variant in California

California Department of Public Health say 35.6% of coronavirus variants sequenced in June have been identified as Delta variant. In May, Delta accounted for just 5.6% of coronavirus cases in California and was the state’s fourth most identified variant. Delta is now more widespread than the previous dominant strain, Alpha, and accounted for 34.3% of coronavirus cases in June. Alpha was the state’s most dominant strain in April and May, outpacing the California variant, now known as Epsilon, which currently occurs in less than 2% of cases.

Los Angeles Times report



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USA: Lions, tigers, bears, chimps, bats and pigs vaccinated against coronavirus

The Oakland Zoo in California has vaccinated tigers, Black bears, Grizzly bears, mountain lions and ferrets against COVID-19 this week and is poised to inoculate chimpanzees, fruit bats and pigs.  The animals are being given experimental doses of the Zoetis vaccine, said Dr. Alex Herman, vice president of veterinary services at Oakland Zoo. The company is donating 11,000 doses to 70 zoos across the United States. report



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USA: 3,620 #coronavirus vaccine breakthrough cases reported in California – up ~600 in one week. 150 hospitalized and at least 20 dead

California has reported 3,620 so-called breakthrough cases of coronavirus infections in people who were fully vaccinated since Jan. 1, state public health officials said Wednesday. That is nearly 600 more breakthrough cases than reported just last week. Of those cases, at least 150 people were hospitalized and at least 20 died.

The 3,620 breakthrough cases represent 0.25% of the more than 1.4 million coronavirus cases reported in California from Jan. 1 to May 5. The 20 deaths make up 0.06% of the 35,677 COVID-19 deaths in that time. report


Seychelles: a population of 100,000 that has 900 #coronavirus vaccine breakthrough cases


Seychelles: a population of 100,000 that has 900 #coronavirus vaccine breakthrough cases


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USA: 3,084 #coronavirus vaccine breakthrough cases in California

Between Jan. 1 and April 28, California public health officials recorded 3,084 breakthrough cases of COVID-19 in people who were fully vaccinated. That’s out of 12.9 million people who were fully vaccinated.  “As more time passes and more people are fully vaccinated, it is likely that additional post-vaccination cases will occur,” the California Department of Public Health said in a statement. “The number of post-vaccination cases remains small.” report


CDC: 9,245 #coronavirus vaccine breakthough cases in the USA


CDC: 9,245 #coronavirus vaccine breakthough cases in the USA



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New SARS-CoV-2 #coronavirus lineage that shares mutations with known Variants of Concern (VOC) reported in 20 states across USA

We report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. This lineage, which we refer to as B.1.x (COG-UK sometimes references similar samples as B.1.324.1), is present in at least 20 states across the USA and in at least six countries. However, a large deletion causes the sequence to be automatically rejected from repositories, suggesting that the frequency of this new lineage is underestimated using public data.

Recent dynamics based on 339 samples obtained in Santa Cruz County, CA, USA suggest that B.1.x may be increasing in frequency at a rate similar to that of B.1.1.7 in Southern California. At present the functional differences between this variant B.1.x and other circulating SARS-CoV-2 variants are unknown, and further studies on secondary attack rates, viral loads, immune evasion and/or disease severity are needed to determine if it poses a public health concern.

BiorXiv preprint:   A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control

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L452R mutation is present in more than 400 SARS-CoV-2 #coronavirus genomes isolated from over 20 countries (and a gorilla in San Diego Zoo too!)

Scientists have examined the Nextstrain and GISAID databases and found that the L452R mutation is present in more than 400 SARS-CoV-2 genomes isolated from over 20 countries. This indicates a strong positive selection for L452R mutation.

The scientists identified L452R amino acid substitution in the spike region as the dominant mutation in specimens collected since November 2020. Specifically, they observed that two independent SARS-CoV-2 variants (CAL.20C and CAL.20A) containing spike L452R mutation emerged recently in the state of California. Of these variants, CAL.20C (clade 20C; lineage B.1.429) is considered to be the predominant variant in California since November 2020. However, the CAL.20A variant (clade 20A; lineage B.1.232) identified in this study has emerged much more recently than CAL.20C and is primarily circulating in California. Based on the phylogenetic analysis, the scientists indicated that L452R mutation is the primary driving force behind the emergence of both variants. Such an increase in L452R mutation frequency in recent SARS-CoV-2 variants directly indicates its crucial involvement in viral adaptive evolution due to positive selection.

Interestingly, they found CAL.20A variant from a gorilla at the San Diego Zoo, which contains two additional mutations in the non-structural protein 2 (NSP2).

In contrast to CAL.20C, no massive clonal expansion was observed for CAL.20A. According to the study findings, CAL.20C contains two additional spike mutations along with L452R, which are missing in CAL.20A. The scientists believe that these additional mutations may be responsible for increasing the adaptive benefits of L452R, and because of this reason, CAL.20A could not achieve the same expansion rate as CAL.20C.

News-Medical,net report

Biorxiv preprint


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California #coronavirus variant CAL.20C accounts for nearly half of COVID-19 cases in Southern California and about a 1/3 of cases in the state

The CAL.20C variant accounts for nearly half of COVID-19 cases in Southern California and about a third of cases in the state based on an analysis of viral genomes posted to a global database called GISAID.

What’s more, the researchers found that by the end of January, the variant had spread to 19 other states, up from five states in November 2020. It has also spread beyond the U.S. to six other countries — Australia, Denmark, Israel, New Zealand, Singapore and the United Kingdom.

Livescience article

Jama Network Paper


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Emergence of a novel #SARSCoV2 strain in Southern California, USA – CAL.20C

“We detected a novel strain descended from cluster 20C and defined by five mutations (ORF1a: I4205V, ORF1b:D1183Y, S: S13I;W152C;L452R)(Figure 1). This strain, CAL.20C, was first observed in July 2020 in 1/1230 samples from LA county and not detected in Southern California again until October. Since then, this strain’s prevalence has increased absolutely and relatively in Southern California, where by December it accounted for 24% of all samples (Figure 2A) and 36.4% (66/181) of our local Los Angeles cohort.”


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Several San Diego gorillas recovering from #COVID19, zoo says

A troop of gorillas at the San Diego Zoo’s Safari Park is recovering from an outbreak of COVID-19 that sickened several of the group’s eight members, the zoo said in a news release on Monday.

The gorillas began to fall ill on Jan. 6, when two of them started coughing, the statement by San Diego Zoo Global said.

The strain that infected them was “a new, highly contagious strain of the coronavirus, recently identified in California,” the zoo said.


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New York Times survey of more than 1,700 American colleges and universities reveals more than 252,000 #coronavirus cases and at least 80 deaths since the pandemic began

Thousands of new coronavirus cases continue to emerge on college campuses. A New York Times survey of more than 1,700 American colleges and universities — including every four-year public institution and every private college that competes in N.C.A.A. sports — has revealed more than 252,000 cases and at least 80 deaths since the pandemic began.

Most of the cases have been announced since students returned to campus for the fall term. Most of the deaths were reported in the spring and involved college employees, not students.

But at least three students — Jamain Stephens, a football player at California University of Pennsylvania; Chad Dorrill, a sophomore at Appalachian State; and Bethany Nesbitt, a student at Grace College — have died in recent weeks after contracting the virus.




Three #California #prison inmates died of #COVID19 in the past week,

Three inmates in California prisons died of COVID-19 in the past week, state prison officials reported, as coronavirus outbreaks continued to devastate the state’s prison population.

The latest death was that of an inmate at Avenal State Prison. He was the 79th incarcerated person in California to die from complications of the illness



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