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


Seychelles: 30% #coronavirus vaccine breakthrough rate


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



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USA: Michigan taxidermist reported infected by mink #coronavirus variant with F486L and N501T mutations

In February 2021, a taxidermist living in Eaton County, Michigan, became infected with COVID-19. A sample from his positive test result was sent to the state lab to be genetically sequenced — and came back as connected to a mutation of the virus found in infected mink, whose fur is used for coats and clothing.

In early February, the linked COVID-19 case involving the Eaton taxidermist was confirmed through genetic testing.

MDHHS confirmed the CDC’s account of the mutations, identifying them as F486L and N501T. Those two mutations have been identified by researchers as the dominant mink COVID-19 strains in the United States, according to a preprint study published last month by two Canadian researchers, and may have evolved in humans before being transmitted to minks, report




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USA: ZooTampa vaccinates animals against #coronavirus

A veterinary pharmaceutical company has developed a coronavirus shot for animals, and ZooTampa at Lowry Park plans to protect the wildlife in its care with the vaccine. Zoo leaders recently decided to use a coronavirus shot developed by veterinary pharmaceutical company Zoetis.

“We’re not worried about birds, we’re not worried about reptiles; we’re only looking at mammals,” said a zoo spokesperson.  “We are told dozens of animals could be on that list to get the vaccine, including primates, felines, bats, and smaller mammals related to the mink family.”

Fox13news report

Gamaleya Institute: ‘The next stage of the epidemic is the infection with the #coronavirus of farm and domestic animals’



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NEJM “a recombination event between B.1.1.7 and B.1.526” #coronavirus variants

Examination of the SARS-CoV-2 sequences revealed that both patients were infected with variant viruses. Rapid identification of sequence variants by targeted PCR amplification showed that neither sequence precisely fit any known clade. Some of the substitutions in Patient 1 (T95I, del144, E484K, A570D, D614G, P681H, and D796H) were shared with B.1.526 (T95I, E484K, and D614G6), and three substitutions were shared with Patient 2 (in whom the variants T95I, G142V and del144, F220I, R190T, R237K, R246T, and D614G were detected). Whole viral genome sequencing revealed several additional substitutions, including D796H, present in a guanine–cytosine–rich region not identified by targeted PCR. These substitutions may decrease sensitivity to convalescent serum11 and may have some unique noncoding changes as compared with the clades first identified in Wuhan, the United Kingdom, and New York City.

Although more detailed analysis of whole-genome sequencing from Patient 1 was undertaken, we could not conclude that the variant in this patient was a Pango lineage because it was only present in a single person.

Its closest links on the phylogenetic tree were the variant first identified in the United Kingdom (B.1.1.7) and the variant first identified in New York City (B.1.526), but with considerable differences. It will be of interest to determine whether this may have resulted from a recombination event between B.1.1.7 and B.1.526, as has been recently reported for recombination between the B.1.1.7 lineage and the “wild-type” lineage first identified in Wuhan. Alternatively, shared substitutions may be the result of convergent evolution.

NEJM: Vaccine Breakthrough Infections with SARS-CoV-2 Variants


See also:

NEJM: In two #coronavirus vaccine breakthrough cases “examination of the SARS-CoV-2 sequences revealed that both patients were infected with variant viruses” .. “neither sequence precisely fit any known clade”

Household transmission of R.1 #coronavirus lineage with spike E484K mutation in Japan

In this study, we conducted genetic surveillance and identified R.1 lineage harboring E484K mutation in RBD by whole genome sequencing. The R.1 lineage was observed in three patients and transmitted among relatives in Japan. To investigate the global distribution of R.1  lineage, we next collected registration data from the EpiCoV of GISAID database [28]. As of March 5, 2021, a total of 305 samples of R.1 lineage had been registered from all over the world, with the majority spread in the USA (44%, 135/305) and Japan (28%, 84/305) (Figure 1A and Table 1). R.1 lineage was first reported in Texas, USA at the end of October 2020, and was found in Japan at the end of November 2020. The number of detected lineages has changed in a similar trend between the USA, Japan and other countries (Figure 1A), implying that SARS-CoV-2 R.1 lineage may have emerged in several regions at approximately the same time.

MedrXIV preprint: Household transmission of SARS-CoV-2 R.1 lineage with spike E484K mutation in Japan

R.1 details above from


See also:

USA: large covid-19 outbreak in Kentucky with R.1 #coronavirus lineage variant after vaccination with Pfizer



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

It is important to note that reported vaccine breakthrough cases will represent an undercount. This surveillance system is passive and relies on voluntary reporting from state health departments which may not be complete. Also, not all real-world breakthrough cases will be identified because of lack of testing. This is particularly true in instances of asymptomatic or mild illness. These surveillance data are a snapshot and help identify patterns and look for signals among vaccine breakthrough cases.

CDC Vaccine Breakthrough information



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USA: New Hampshire reports 52 vaccine breakthrough cases, 2 have died

New Hampshire has identified 52 vaccine breakthrough cases with additional suspected cases under investigation, said Jake Leon, spokesman for the Department of Health and Human Services. Of those 52 cases, two people have died, Leon said.

Nationally over 7,157 of the 87 million people vaccinated had a breakthrough illness as of April 20 and one percent of that group had died, according to the Centers for Disease Control. The CDC says women make up 64 percent of the breakthrough cases; above age 60 it was 46 percent of the cases, and having an asymptomatic infection was found in 31 percent of the cases. report



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B1427/B1429 are listed as Variants of Concern by the CDC, as Variants of Interest (VOI) by WHO

The World Health Organization lists as B.1.427 and B.1.429 as Variants of Interest. The CDC website, however, lists B.1.427 and B.1.429 as Variants of Concern along with B.1.1.7 (UK variant), P.1 (Brazilian Variant) and B.1.351 (South African Variant).


CDC:  SARS-CoV-2 Variant Classifications and Definitions

WHO: COVID-19 Weekly Epidemiological Update




USA: large covid-19 outbreak in Kentucky with R.1 #coronavirus lineage variant after vaccine breakthrough with Pfizer

The Kentucky Department for Public Health and a local health department investigated a COVID-19 outbreak in a skilled nursing facility that occurred after all residents and health care personnel had been offered vaccination. Among 83 residents and 116 health care personnel, 75 residents and 61 staff, respectively, received 2 vaccine doses. Twenty-six residents and 20 health care personnel received positive test results for SARS-CoV-2, the virus that causes COVID-19, including 18 residents and four health care personnel who had received their second vaccine dose >14 days before the outbreak began.

An R.1 lineage variant was detected with whole genome sequencing. Although the R.1 variant has multiple spike protein mutations, vaccinated residents and HCP were 87% less likely to have symptomatic COVID-19 compared with those who were unvaccinated. Vaccination of skilled nursing facility populations, including health care personnel, is critical to reduce the risk for SARS-CoV-2 introduction, transmission, and severe outcomes in skilled nursing facilities.

CDC report:  COVID-19 Outbreak Associated with a SARS-CoV-2 R.1 Lineage Variant in a Skilled Nursing Facility After Vaccination Program — Kentucky, March 2021

See also:

Household transmission of R.1 #coronavirus lineage with spike E484K mutation in Japan



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USA, CDC and FDA: 15 cases of thrombosis-thrombocytopenia syndrome (TTS) reported, numbers double in one week

FDA and CDC have recommended lifting the pause on Johnson & Johnson (Janssen) COVID-19 Vaccines in the USA. 

On April 13, the FDA and CDC announced that, out of more than 6.8 million doses administered, six reports of a rare and severe type of blood clot combined with low blood platelet levels occurring in people after receiving the Janssen COVID-19 Vaccine had been reported to VAERS. In these cases, a type of blood clot called cerebral venous sinus thrombosis (CVST) was seen in combination with low levels of blood platelets (thrombocytopenia). 

Today, the agencies can confirm that a total of 15 cases of TTS have been reported including the original six reported cases. All of these cases occurred in women between the ages of 18 and 59, with a median age of 37 years. Reports indicated symptom onset between 6 and 15 days after vaccination. report



CDC: 7,157 #coronavirus vaccine breakthrough cases with 88 deaths reported in the US

The US CDC has reported 7,157 vaccine breakthrough cases for Covid-19 vaccines as of 20th April 2021. 64% of the cases were found in females, 46% were aged over 60yrs, and 38% of the infections were asymptomatic. There were 88 deaths reported.

CDC: COVID-19 Breakthrough Case Investigations and Reporting

See also: 819 coronavirus vaccine breakthrough cases recorded by Colorado State epidemiologist


USA: 819 #coronavirus vaccine breakthrough cases recorded by Colorado State epidemiologist

State epidemiologist says the state recorded 819 breakthrough cases out of 106,965 total cases from the end of January through April 19. Colorado health officials say they studied what they call “breakthrough cases” of Coloradans who got the coronavirus after getting vaccinated. report


See also: 7,157 coronavirus vaccine breakthrough cases with 88 deaths reported in the US



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USA: New Texas #coronavirus variant BV-1 shows signs of antibody resistance and more severe illness in young people

Scientists at Texas A&M University’s Global Health Research Complex say they’ve detected a new Covid-19 variant that shows signs of a more contagious strain that causes more severe illness and appears to be resistant to antibodies.

The new variant, BV-1, named after its Brazos Valley origin, was found during Texas A&M’s routine coronavirus screening via saliva sample in a young student who had mild cold-like symptoms. The student tested positive for Covid on March 5 and tested positive again on March 25, showing that the new strain may cause a longer infection in younger people. The student’s symptoms resolved by April 2 and a third test on April 9 came back negative.

CNBC news report


** Update** Two more new variants have been discovered by A&M – BV-2 and BV-3, named for the Brazos Valley – were recently identified from samples collected from on campus testing of students and faculty. Mandatory COVID-19 saliva testing for students living, studying, or working on the Texas A&M University campus in Bryan-College Station began back in March. report


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UK #coronavirus variant B.1.1.7 may not have evolved spontaneously in the UK or within human populations

“Here we analyzed 454,443 SARS-CoV-2 spike genes/proteins and 14,427 whole-genome sequences. We demonstrated that the early variant B.1.1.7 may not have evolved spontaneously in the United Kingdom or within human populations. Our extensive analyses suggested that Canidae, Mustelidae or Felidae, especially the Canidae family (for example, dog) could be a possible host of the direct progenitor of variant B.1.1.7.”

Biorxiv preprint: Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2



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