USA: AY.3 genomes increasing faster than Delta B.1.617.2

A long and detailed Twitter thread by Vinod Scaria on the rise of the AY.3 Delta plus variant in the USA which seems to be outcompeting Delta B.1.672 in some states. Outbreak.info is showing that AY.3 genomes are found in 37% of recent sequences.

 

 

 

Github: AY.3.1 – a new sub-lineage of AY.3 concentrated in Mississippi, USA

USA: Cape Cod superspreader – 79% of breakthrough infections symptomatic, 80% of hospitalized were fully vaccinated

Scientists researching the Provincetown, Cape Cod Covid outbreak reported that 79 percent of the breakthrough infections were symptomatic. Four of five people who were hospitalized were fully vaccinated.

The CDC study “raises the very worrisome possibility that high viral loads can occur in people who have Delta, and this is a fundamental as we have to approach the fall and winter,” said David O’Connor, a professor of pathology and laboratory medicine at the University of Wisconsin School of Medicine and Public Health.

Washington Post report

 

 

Image by Mark Martins from Pixabay

USA: Washington State Vaccine Breakthroughs by Variant up to 28th July 2021

This week’s update from Washington State showing vaccine breakthrough cases and which Sars-CoV-2 variant is causing them up to 28th July 2021. Of note this week is huge jump for Delta B.1.617.2 breakthrough cases, which have more than doubled in one week from 113 to 254. There are further increases in vaccine breakthroughs for other variants too.

Vaccine Breakthroughs up to 28th July 2021

28th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.733734%43%29
GammaP.116817%10%12
EpsilonB.1.42911612%15%3
DeltaB.1.617.225426%7%141
IotaB.1.526263%3%4
BetaB.1.351101%1%0
EpsilonB.1.427111%2%0
EtaB.1.52540%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther546%18%4
Total981100%100%193

Vaccine Breakthroughs up to 21st July 2021

21st July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730839%44%-1
GammaP.115620%10%9
EpsilonB.1.42911314%16%0
DeltaB.1.617.211314%4%23
IotaB.1.526223%3%0
BetaB.1.351101%1%-1
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther506%19%0
Total788100%100%30

Vaccine Breakthroughs up to 14th July 2021

14th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730941%44%12
GammaP.114719%10%6
EpsilonB.1.42911315%16%0
DeltaB.1.617.29012%4%20
IotaB.1.526223%3%1
BetaB.1.351111%1%0
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther496%20%0
Total757100%100%39

 

USA: Washington State Vaccine Breakthroughs by Variant up to 21st July 2021

 

So what is Plan B if the vaccines fail with a new #coronavirus super-variant?

Image by David Mark from Pixabay

CNN: CDC fails to publish data needed to judge risk of breakthrough infection

“The CDC has tracked serious infections requiring hospitalization and deaths among fully vaccinated people. But it’s not publishing that data in a timely manner, and it has stopped national tracking of mild and asymptomatic infections. That makes it hard to know if fully vaccinated people are, in fact, less likely to pass along the infection to others. It’s hard to say whether people infected with the Delta variant despite having been vaccinated are more likely to infect others.”

CNN opinion piece

Update:  The Centers for Disease Control and Prevention doesn’t have enough resources to properly track Covid-19 “breakthrough cases,” Dr. Scott Gottlieb told CNBC’s “Squawk Box” on Wednesday.

 

 

Image by Sasin Tipchai from Pixabay

Mink found infected with Covid-19 after they escaped their cages on Farm in British Columbia, Canada

Canada: Two mink test positive for Covid-19 – four mink found roaming farm after escaping their cages

Two more mink have tested positive for the COVID-19 virus from a Fraser Valley, British Columbia, farm already under quarantine from positive tests in May. In this instance, four mink had escaped their cages and were captured on the farm.

As a result of the new infections, a moratorium has been placed on any new mink farms in B.C., with a cap on existing mink farms at current numbers. 

Three B.C. mink farms have had animals test positive since December 2020. “All three remain under quarantine, with no mink being moved to or from the properties.”

Cowichanvalleycitizen.com report

 

Mink: 100% infection, recovery and then 75% re-infection of farmed mink

 

Brazil: previously infected and fully vaccinated subjects with high anti-S IgG titers are susceptible to infection by VOC

Here we show that even previously infected and fully vaccinated subjects with high anti-S IgG titers are susceptible to infection by VOC, highlighting that immune responses induced by either natural infection or vaccination may not be sufficient to prevent infection by SARS-CoV-2 variants.

For this study we selected 72 SARS-CoV-2 recently tested positive individuals with nasopharyngeal swabs collected between mid-January and March 2021 with SARS-CoV-2 RT-qPCR Ct values <30. These include both cancer patients and healthcare workers (HCW) from the Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil. Of those 72 subjects, six were vaccinated prior the current infection and two out of those six were also reinfection cases. Another three subjects also represented reinfections, showing a previous infection during the first wave of the pandemic in Brazil.

Six HCW included in this study have been fully or partially vaccinated with one of the vaccines available in Brazil, either CoronaVac (Sinovac/Butantã) or ChAdOx1-S/nCoV-19 (AstraZeneca/Oxford/Fiocruz). All six tested positive for SARS-CoV-2 RT-qPCR after at least one vaccine dose and reported mild symptoms during infection.

ScienceDirect.com preprint: New infections by SARS-CoV-2 variants of concern after natural infections and post-vaccination in Rio de Janeiro, Brazil

 

 

 

Image by Rafael Moura Sb. from Pixabay

Indonesia: Mortality rate in children as high as 40% in PCR confirmed Covid-19 cases

During the study period, 490 [child] patients were admitted and diagnosed with suspected and probable COVID-19. Of these patients, 50 (10.2%) were confirmed to have COVID-19, and 20 (40%) had a fatal outcome.

The fatality rate was higher in patients aged ≥10 years, categorized with severe disease upon admission, PaO2/FiO2 ratio ≤300 mmHg and chronic underlying diseases. The most common clinical manifestations were generalized symptoms, while acute respiratory distress syndrome (8/20) and septic shock (7/20) were the two most common causes of death. Increased procalcitonin, D-dimer, lactate dehydrogenase and presepsin levels were found in all fatal cases. One patient met the criteria of multisystem inflammatory syndrome in children.

Conclusion: Our work highlights the high mortality rate in paediatric patients with positive SARS-CoV-2 polymerase chain reaction test. These findings might be related to or co-incided with COVID-19 infection. Further studies are needed to improve understanding of the role of severe acute respiratory syndrome coronavirus-2 in elaborating the mechanisms leading to death in children with comorbidities.

Pubmed paper: Mortality in children with positive SARS-CoV-2 polymerase chain reaction test: Lessons learned from a tertiary referral hospital in Indonesia 

See also:

NYtimes report: Children Are Dying as Virus Surges in Indonesia – hundreds have died from Covid-19 in recent weeks, many of them under the age of 5.

 

 

 

Image by Fikih Firmansyah from Pixabay

 

UK: Third Covid-19 wave is the worst yet

The peak of the second Alpha wave was the 9th January 2021. Interactive maps produced by the UK government show infections in the third Delta wave are clearly worse than the peak of the second wave despite the “wall of protection” supposedly offered by the vaccines.

The official Covid-19 figures, the hospitalizations and the deaths have yet to catch up with what is happening on the ground.

 

UK: ONS estimates over 800,000 had Covid-19 this week

USA: Washington State Vaccine Breakthroughs by Variant up to 21st July 2021

This week’s update from Washington State showing vaccine breakthrough cases and which Sars-CoV-2 variant is causing them. Of note this week is another large jump for Delta B.1.617.2 breakthrough cases, and a further increase for Gamma P1 breakthroughs.

Vaccine Breakthroughs up to 21st July 2021

21st July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730839%44%-1
GammaP.115620%10%9
EpsilonB.1.42911314%16%0
DeltaB.1.617.211314%4%23
IotaB.1.526223%3%0
BetaB.1.351101%1%-1
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther506%19%0
Total788100%100%30

Vaccine Breakthroughs up to 14th July 2021

14th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730941%44%12
GammaP.114719%10%6
EpsilonB.1.42911315%16%0
DeltaB.1.617.29012%4%20
IotaB.1.526223%3%1
BetaB.1.351111%1%0
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther496%20%0
Total757100%100%39

Israel: 90% of confirmed Covid-19 cases in the over-fifties are fully vaccinated

The Covid vaccine may be losing its efficacy in older people, researchers in Israel have warned. The monitoring team at the Hebrew University in Jerusalem reported that about 90 per cent of new confirmed cases in the over-fifties group were people who had been fully vaccinated. “It seems there’s a reduced efficiency of the vaccine, at least for part of the population,” the team said.

The Times report

 

UK: vaccine breakthroughs now nearly HALF of all new Covid-19 cases

 

Image by PublicDomainPictures from Pixabay

Bangladesh: new study shows 80% percent of children infected by Delta are under 10 years of age

The Chittagong study included children from newborns to 18-year-olds infected with coronavirus. The study found that 80 percent of the affected children are under 10 years of age. Delta variants have been identified in infants as young as eight months old.

The Sars-CoV-2 Delta variant is increasing corona infection among children in Chittagong. Of the 12 children who were recently selected for the coronavirus study, all were found to be infected with the Delta variant. The data was obtained by sequencing the genomes of 12 randomly selected children from Chittagong Maternal and Child Hospital and Chittagong General Hospital in the first week of June to July.

According to another study by the research team, 80 percent of adult Covid-19 patients are men, but children are the exception. Children are equally infected and infected with this variant. The presence of this variant was observed in 50 percent of boys and 50 percent of girls. Ninety-five percent of the children had fever and 60 percent had a cold and cough. However, one child was completely asymptomatic.

The head of the Corona unit of the General Hospital, Abdur Rab Masum said, “It is a matter of great concern that the level of covid among children is increasing. In this case, the need for specialized intensive care centers for children may increase in the coming days and the whole family should be more vigilant in the interest of children.

The Dailystar.net report

 

 

Image by Maruf Rahman from Pixabay

UK: Hebburn West in South Tyneside now at nearly 2,000 coronavirus cases per 100,000 people

When we looked at the coronavirus situation in West Hebburn in South Tyneside a week ago we were astonished by the infection rates in that part of North East England, which, at that point, were 1,555 per 100,000 people. Well, one week later, things, it seems, have gone from bad to worse with the infection level now at 1,983.5 cases per 100,000 people in West Hebburn.  We’re not sure if that is a UK record for infection levels, but is certainly the highest rate we have ever seen for the UK. And this is two days BEFORE “Freedom Day” on the 19th July 2021, after which all mitigations and restrictions on gatherings will be lifted in the UK.

Last week…

UK: Hebburn West, South Tyneside now at 1,555 coronavirus cases per 100,000 people

 

WHO: “Allowing #SARSCoV2 to spread & infect others by not implementing consistently proven actions that prevent infections, reduce spread, prevent disease & save lives is immoral, unethical, & non-scientific”

 

UK: Vaccine Breakthrough for Health Minister Sajid Javid

Sajid Javid, who became UK health secretary in June, said he had taken a lateral flow test after feeling a “bit groggy” on Friday night and it was positive. He said he was now self-isolating until he got the results of a PCR test. In a video posted on his Twitter feed, Mr Javid said: “I was feeling a bit groggy last night, so I took a lateral flow test this morning and it’s come out positive, so I’m now self-isolating at home with my family until I get the results of a PCR test.”  “I’m grateful that I’ve had two jabs of the vaccine and so far my symptoms are very mild.”

BBC report

 

UK: vaccine breakthroughs now nearly HALF of all new Covid-19 cases

USA: Washington State Vaccine Breakthroughs by Variant up to 14th July 2021

Updated figures from Washington State showing vaccine breakthrough cases by the Sars-CoV-2 variant causing them up to 14th July 2021. Some changes from the previous file, notably another increase for both Alpha and Delta breakthroughs, with Delta increasing from 10% to 12% of cases.

Vaccine Breakthroughs up to 14th July 2021

14th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730941%44%12
GammaP.114719%10%6
EpsilonB.1.42911315%16%0
DeltaB.1.617.29012%4%20
IotaB.1.526223%3%1
BetaB.1.351111%1%0
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther496%20%0
Total757100%100%39

 

PREVIOUS WEEK: Vaccine Breakthroughs up to 7th July 2021

7th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Number Increase
From Previous
Week
AlphaB.1.1.729741%44%11
GammaP.113919%9%6
EpsilonB.1.42911316%16%0
DeltaB.1.617.27010%4%30
IotaB.1.526213%3%7
BetaB.1.351112%1%1
EpsilonB.1.427112%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
Other497%20%0
Total716100%100%55

 

USA: Washington State Vaccine Breakthroughs by Variant up to 7th July 2021

 

USA: vaccine breakthough cases in Washington State by coronavirus variant to 30th June 2021

 

Image by David Mark from Pixabay