India: 16% vaccine breakthrough in Delhi hospital #coronavirus study

A small-scale study on 113 healthcare workers who had received at least one vaccine dose at a private hospital in Delhi found that 18 tested positive for Covid but all except one had mild symptoms.  Of the 113 in the study, 107 had received the second dose of the vaccine.

Taken in percentage form, the study found that breakthrough infections — Covid infection in vaccinated individuals — occurred in 15.9 per cent (18 persons) of the vaccinated individuals and 95 per cent had mild symptoms. Of these, 17 incurred the infection after the second dose. According to the study, of the breakthrough infections in 18 persons, 17 incurred the infection after the second dose. These 17 had got their second dose after a mean of 34.8 days following the first jab.

NDTV report

Belgium: Five fully vaccinated care home residents infected with B.1.617.3 in vaccine breakthrough outbreak

Seychelles: 30% #coronavirus vaccine breakthrough rate

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Belgium: Five fully vaccinated care home residents infected with B.1.617.3 in vaccine breakthrough outbreak

Five residents of a care home in Borsbeek in Antwerp province have been infected with the so-called Indian variants of Covid-19, according to the Flemish Agency for Health and Care. One of those affected has died.  All of the home’s residents have been fully vaccinated.

In three of the cases involved in the new outbreak, the Indian variant has been confirmed, and it is supposed the same goes for the other two. One has since died, and another is in hospital.

Brussels Times report

 

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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.”

Sacbee.com report

 

Seychelles: 30% #coronavirus vaccine breakthrough rate

 

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

 

 

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Seychelles: 30% #coronavirus vaccine breakthrough rate

The Seychelles, which has fully vaccinated over 60% of its population against Covid-19, is bringing back restrictions amid a rise in cases. The archipelago of nearly 100,000 people recorded close to 500 new cases in the three days to 1 May and has about 1,000 active cases. A third of the active cases involved people who have had two vaccine doses, the country’s news agency said. The rest had either had a single dose or were unvaccinated.

BBC.co.uk report

There are currently 1,068 active Covid cases in the Seychelles, of which a third have been detected in people given two doses of either AstraZeneca’s or China’s Sinopharm’s vaccine.  It unclear what has triggered the surge in cases but testing has detected the South African variant spreading on the islands.  (Daily Mail report)

 

Graph courtesy of Ourworldindata.org

 

 

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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 COV-lineages.org

 

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.

Patch.com report

 

 

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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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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.

Denver.cbslocal.com report

 

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

 

 

Photo by Henry Desro on Unsplash

 

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”

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).

NEJM article  “Vaccine Breakthrough Infections with SARS-CoV-2 Variants”

 

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New Zealand: fully vaccinated airport worker tests positive for #coronavirus

The Auckland Airport worker who has tested positive for Covid-19 cleans planes from high risk Covid-19 ‘red-zone countries’, and had been fully vaccinated, Prime Minister Jacinda Ardern says. They were fully vaccinated early on in the campaign and were last tested on 12 and 19 April, she said. Yesterday’s test returned a positive result today.

“The reason this person was part of our surveillance testing was because they were working in an area we consider to be high-risk. They are coming in contact with the planes that are carrying passengers from high risk countries and so that is a place where our workers, they are in the kinds of roles that means they need to be tested, they need to be vaccinated, but they also need to be thanked for the jobs that they do because of the risk that it carries.”

RNZ.co.nz report

 

 

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UK: #coronavirus vaccine breakthrough cases reported with B.1.351 and B.1.1.7 variants

People in the UK have been infected with Covid-19 more than once thanks to catching different variants of the coronavirus. Dr Susan Hopkins, chief medical adviser for NHS Test and Trace, said there had been cases where people had become reinfected by different strains of the coronavirus. “We have seen some people who have had their first dose of vaccine who have had the South African variant and the variant that arose in Kent,” she told BBC’s the Andrew Marr show. “You can see that they’re not as good against the South African variant as they are against our own (variant) B117 at preventing infection and transmission.”

KentLive.new report

 

 

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