Category: Genome
USA: Washington State Vaccine Breakthroughs by Variant up to 4th August 2021
This week’s update from Washington State showing vaccine breakthrough cases and which Sars-CoV-2 variant is causing them up to 4th August 2021. Of note this week is another big jump for Delta B.1.617.2 vaccine breakthrough cases, which have increased from 254 to 405 in one week. Delta is now responsible for more breakthrough cases in Washington State than any other variant. There are also further small increases in vaccine breakthrough cases for the Alpha and Gamma variants.
Vaccine Breakthroughs up to 4th August 2021
| 4th August 2021 Variant | Lineage | Number 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 |
|---|---|---|---|---|---|
| Delta | B.1.617.2 | 405 | 35% | 10% | 151 |
| Alpha | B.1.1.7 | 343 | 30% | 41% | 6 |
| Gamma | P.1 | 175 | 15% | 9% | 7 |
| Epsilon | B.1.429 | 116 | 10% | 15% | 0 |
| Iota | B.1.526 | 27 | 2% | 3% | 1 |
| Epsilon | B.1.427 | 11 | 1% | 2% | 0 |
| Beta | B.1.351 | 10 | 1% | 1% | 0 |
| Eta | B.1.525 | 4 | 0% | 0% | 0 |
| Kappa | B.1.617.1 | 1 | 0% | 0% | 0 |
| Other | Other | 50 | 4% | 19% | -4 |
| Total | 1142 | 100% | 100% | 161 |
Vaccine Breakthroughs up to 28th July 2021
| 28th July 2021 Variant | Lineage | Number 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 |
|---|---|---|---|---|---|
| Alpha | B.1.1.7 | 337 | 34% | 43% | 29 |
| Gamma | P.1 | 168 | 17% | 10% | 12 |
| Epsilon | B.1.429 | 116 | 12% | 15% | 3 |
| Delta | B.1.617.2 | 254 | 26% | 7% | 141 |
| Iota | B.1.526 | 26 | 3% | 3% | 4 |
| Beta | B.1.351 | 10 | 1% | 1% | 0 |
| Epsilon | B.1.427 | 11 | 1% | 2% | 0 |
| Eta | B.1.525 | 4 | 0% | 0% | 0 |
| Kappa | B.1.617.1 | 1 | 0% | 0% | 0 |
| Zeta | P.2 | 0 | 0% | 0% | 0 |
| Other | Other | 54 | 6% | 18% | 4 |
| Total | 981 | 100% | 100% | 193 |
Vaccine Breakthroughs up to 21st July 2021
| 21st July 2021 Variant | Lineage | Number 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 |
|---|---|---|---|---|---|
| Alpha | B.1.1.7 | 308 | 39% | 44% | -1 |
| Gamma | P.1 | 156 | 20% | 10% | 9 |
| Epsilon | B.1.429 | 113 | 14% | 16% | 0 |
| Delta | B.1.617.2 | 113 | 14% | 4% | 23 |
| Iota | B.1.526 | 22 | 3% | 3% | 0 |
| Beta | B.1.351 | 10 | 1% | 1% | -1 |
| Epsilon | B.1.427 | 11 | 1% | 2% | 0 |
| Eta | B.1.525 | 4 | 1% | 0% | 0 |
| Kappa | B.1.617.1 | 1 | 0% | 0% | 0 |
| Zeta | P.2 | 0 | 0% | 0% | 0 |
| Other | Other | 50 | 6% | 19% | 0 |
| Total | 788 | 100% | 100% | 30 |
Vaccine Breakthroughs up to 14th July 2021
| 14th July 2021 Variant | Lineage | Number 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 |
|---|---|---|---|---|---|
| Alpha | B.1.1.7 | 309 | 41% | 44% | 12 |
| Gamma | P.1 | 147 | 19% | 10% | 6 |
| Epsilon | B.1.429 | 113 | 15% | 16% | 0 |
| Delta | B.1.617.2 | 90 | 12% | 4% | 20 |
| Iota | B.1.526 | 22 | 3% | 3% | 1 |
| Beta | B.1.351 | 11 | 1% | 1% | 0 |
| Epsilon | B.1.427 | 11 | 1% | 2% | 0 |
| Eta | B.1.525 | 4 | 1% | 0% | 0 |
| Kappa | B.1.617.1 | 1 | 0% | 0% | 0 |
| Zeta | P.2 | 0 | 0% | 0% | 0 |
| Other | Other | 49 | 6% | 20% | 0 |
| Total | 757 | 100% | 100% | 39 |
Image by Deborah Jackson from Pixabay
Preprint: C.37 Lambda variant exhibits higher infectivity and immune resistance
“In this study, we demonstrated that three mutations, the RSYLTPGD246-253N, L452Q and F490S mutations, respectively confer resistance to the vaccine-induced antiviral immunity. Additionally, the T76I and L452Q mutations contribute to enhanced viral infectivity. Our data suggest that there are at least two virological features on the Lambda variant: increasing viral infectivity (by the T76I and L452Q mutations) and exhibiting resistance to antiviral immunity (by the RSYLTPGD246-253N, L452Q and F490S mutations).”
BiorXiv preprint: SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance
Image by mailanmaik from Pixabay
Github: AY.3.1 – a new sub-lineage of AY.3 concentrated in Mississippi, USA
AY.3 is the main variant being sequenced weekly in Mississippi (>70% of all recent sequences), most falling within this sub-lineage of AY.3 that is distinguished by the mutations described below (>60% of all recent sequences). For example, of 91 Pangolin-typeable sequences generated on 13 July 2021 by Dr. Robinson’s team, from broad sampling across Mississippi, 68 are AY.3 and 13 are unclassified B.1.617.2. Of those 81 Delta sequences, 60 are this new sub-lineage (those sequences are not yet in GISAID and are thus not included in the counts above for the USA or MS). Thus, there is clear epidemiological relevance of this sub-lineage in a region of the USA.
Github: A new sub-lineage of AY.3 concentrated in Mississippi, US
Image by Mark Dawdy from Pixabay
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.
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 | Lineage | Number 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 |
|---|---|---|---|---|---|
| Alpha | B.1.1.7 | 337 | 34% | 43% | 29 |
| Gamma | P.1 | 168 | 17% | 10% | 12 |
| Epsilon | B.1.429 | 116 | 12% | 15% | 3 |
| Delta | B.1.617.2 | 254 | 26% | 7% | 141 |
| Iota | B.1.526 | 26 | 3% | 3% | 4 |
| Beta | B.1.351 | 10 | 1% | 1% | 0 |
| Epsilon | B.1.427 | 11 | 1% | 2% | 0 |
| Eta | B.1.525 | 4 | 0% | 0% | 0 |
| Kappa | B.1.617.1 | 1 | 0% | 0% | 0 |
| Zeta | P.2 | 0 | 0% | 0% | 0 |
| Other | Other | 54 | 6% | 18% | 4 |
| Total | 981 | 100% | 100% | 193 |
Vaccine Breakthroughs up to 21st July 2021
| 21st July 2021 Variant | Lineage | Number 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 |
|---|---|---|---|---|---|
| Alpha | B.1.1.7 | 308 | 39% | 44% | -1 |
| Gamma | P.1 | 156 | 20% | 10% | 9 |
| Epsilon | B.1.429 | 113 | 14% | 16% | 0 |
| Delta | B.1.617.2 | 113 | 14% | 4% | 23 |
| Iota | B.1.526 | 22 | 3% | 3% | 0 |
| Beta | B.1.351 | 10 | 1% | 1% | -1 |
| Epsilon | B.1.427 | 11 | 1% | 2% | 0 |
| Eta | B.1.525 | 4 | 1% | 0% | 0 |
| Kappa | B.1.617.1 | 1 | 0% | 0% | 0 |
| Zeta | P.2 | 0 | 0% | 0% | 0 |
| Other | Other | 50 | 6% | 19% | 0 |
| Total | 788 | 100% | 100% | 30 |
Vaccine Breakthroughs up to 14th July 2021
| 14th July 2021 Variant | Lineage | Number 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 |
|---|---|---|---|---|---|
| Alpha | B.1.1.7 | 309 | 41% | 44% | 12 |
| Gamma | P.1 | 147 | 19% | 10% | 6 |
| Epsilon | B.1.429 | 113 | 15% | 16% | 0 |
| Delta | B.1.617.2 | 90 | 12% | 4% | 20 |
| Iota | B.1.526 | 22 | 3% | 3% | 1 |
| Beta | B.1.351 | 11 | 1% | 1% | 0 |
| Epsilon | B.1.427 | 11 | 1% | 2% | 0 |
| Eta | B.1.525 | 4 | 1% | 0% | 0 |
| Kappa | B.1.617.1 | 1 | 0% | 0% | 0 |
| Zeta | P.2 | 0 | 0% | 0% | 0 |
| Other | Other | 49 | 6% | 20% | 0 |
| Total | 757 | 100% | 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
Greece: A Delta-like wave of infections caused by a resurgent Alpha variant
Greece’s daily coronavirus cases passed the 3,000 mark on Tuesday, recording a two-month high, as the country struggles with a new surge in infections. In its bulletin, the National Organization for Public Health (EODY) said it had confirmed 3,109 cases in the past 24 hours, which is the highest number since May 11. EODY said four patients died of Covid-19 with the number of fatalities since the start of the pandemic reaching 12,806. At the same time, there are 133 intubated patients in the Intensive Care Units from 139 on Monday.
The Delta variant still hasn’t made much of an impact in Greece yet. The dominant variant is still the Alpha variant B.1.1.7, with some case of B.1.1.318 being found.
Charts courtesy of OurWorldinData.org and Outbreak.info
UK: Vaccine breakthroughs now one third of all new Covid-19 cases
According to the UK ZOE COVID Study, among unvaccinated people in the UK there are currently 22,638 new daily symptomatic cases of COVID on average. Among partly or fully vaccinated people there are currently 11,084 new daily symptomatic cases, an increase of 85% from last week. The positivity rate is still much higher in those with just a first dose, compared to those who are double vaccinated
Latest:
UK: vaccine breakthroughs now nearly HALF of all new Covid-19 cases
Spain: 6 pet ferrets found infected with #coronavirus
We studied 71 ferrets belonging to 7 owners; the ferrets were used as working animals for rabbit hunting in Ciudad Real Province, central Spain. All 71 ferrets were included in the study, and none showed clinical signs of any illness. Group sizes ranged from 4 to 21 (mean 10). Twenty ferrets belonging to groups 1 and 2 were resampled 66 days after initial sampling. Information on coronavirus disease in the owners was not available. Sampling took place during August–November 2020.
We found SARS-CoV-2 RNA in swab samples from 6 of the 71 ferrets.
We conclude that natural SARS-CoV-2 infection in kept ferrets does occur in circumstances of high viral circulation in the human population However, the high cycle thresholds observed and the lack of virus-positive ferrets at resampling suggest that small ferret populations are less able to maintain prolonged virus circulation than large, farmed mink populations.
Photo by Nathaniel Yeo on Unsplash
Belgium: 90-year-old woman coinfection with Alpha and Beta coronavirus variants
Researchers in Belgium report on the case of a 90-year-old woman who was simultaneously infected with two different variants of concern (VOCs) of COVID-19, in a Case Report being presented at the European Congress of Clinical Microbiology & Infectious Diseases (ECCMID) held online this year.
On March 3 2021, the woman, whose medical history was unremarkable, was admitted to the OLV Hospital in the Belgian city of Aalst after a spate of falls. She tested positive for COVID-19 on the same day. She lived alone and received nursing care at home, and had not been vaccinated against COVID-19.
Initially, there were no signs of respiratory distress and the patient had good oxygen saturation. However, she developed rapidly worsening respiratory symptoms, and died five days later.
When the patient’s respiratory sample was tested for VOCs with PCR, they discovered that she had been infected by two different strains of the virus–one which originated in the UK, known as B.1.1.7 (Alpha), and another that was first detected in South Africa (B.1.351; Beta).
The presence of both strains was confirmed by PCR on a second respiratory sample, by sequencing of the S-gene and by whole genome sequencing.
Delta in England: The vaccine breakthrough rate is increasing and Delta is proportionally more deadly for the fully vaccinated than the unvaccinated
Some very surprising news from PHE Technical Briefings which show that the vaccine breakthrough rate in England has increased dramatically over the last 5 weeks, and worse, that the mortality rate for the fully vaccinated cases is proportionally far worse than the mortality rate for the unvaccinated, and that that proportion is also increasing.
We are highlighting the key parts of the PHE documents here, along with a summary of the main findings to make these points clearer.
Please note that the vaccine breakthrough figures we are quoting from PHE are for those vaccinated with two doses and do not include the breakthrough figures for those cases who have had just one dose of the vaccine (in which case the figure would be higher).
No breakdown for which vaccine is responsible for the breakthrough cases is given in the PHE documents. The vaccine breakthrough rate is calculated against all Delta cases, not just those from the last 28 days (in which case the figure would be higher).
Summary:
Sources:
Update: Kit Yates has a stab at explaining this unexpected data in this article “Most COVID deaths in England now are in the vaccinated – here’s why that shouldn’t alarm you”
UK: Vaccine breakthroughs now one third of all new Covid-19 cases
USA: Washington State Vaccine Breakthroughs by Variant up to 7th July 2021
UK: PHE Technical Briefing and Variants of Concern update 18
PHE England have recently published new reports on the SARS-COV-2 variants circulating in Britain: Alpha, Beta, Gamma, Zeta, Eta, B.1.1.318, Theta, Kappa, B.1.617.3, AV.1, C.36.3, Lambda, C.37
SARS-CoV-2 variants of concern and variants under investigation in England
Variants under surveillance
Variant prevalence
Secondary attack rates
SARS-CoV-2 Immunity and Reinfection Evaluation (the SIREN study) cohort monitoring
Part 2: Delta (B.1.617.2) surveillance
Surveillance through genomic data
Delta with K417N (Delta-AY.1)
Investigation of SARS-CoV-2 variants of concern: routine variant data update
Data on individual variants
Alpha
Beta
Gamma
International Epidemiology
Zeta
Eta
VUI-21FEB-04 (B.1.1.318)
Theta
Kappa
VUI-21APR-03 (B.1.617.3)
VUI-21MAY-01 (AV.1)
VUI-21MAY-02 (C.36.3)
Lambda (C.37, VUI-21JUN-01)
Preprint: Transmission event of Delta coronavirus variant reveals multiple vaccine breakthrough infections
Here we describe a transmission of a Delta variant containing SARS-CoV-2 strain, between family members associated with events surrounding a wedding with 92 attendees, near Houston, Texas. Attendance required guests be fully vaccinated and took place outdoors in a large, open-air tent. To date, 6 individuals have tested positive for SARS-CoV-2, all patients were symptomatic, one patient severely enough to receive monoclonal antibody infusion treatment (Regeneron Pharmaceuticals Inc.) and one patient has died.
Encounter timings and viral sequence similarities suggest the strain containing the Delta variant was transmitted to wedding guests from two patients travelling from India. With no history of vaccine failure in these patients, our observations suggest these are true cases of vaccine breakthrough, mediated by the Delta variant.
Full Medrxiv Preprint: Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections
Israel: Hebrew University study finds Pfizer vaccine just 70% effective against Delta variant
Israel: Pfizer vaccine effectiveness against coronavirus infection has dropped to just 64%
Image by Free-Photos from Pixabay
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.
Photo by Mattia Bericchia on Unsplash
USA: vaccine breakthough cases in Washington State by coronavirus variant to 30th June 2021
Washington State has recently published an update on the number of vaccine breakthrough cases. Importantly, it shows which Sars-CoV-2 variant is responsible for 661 of those cases through genome sequencing. This hugely important information is not available for most states in the USA, so the fact that Washington State continues to publish this information for the Covid variants currently circulating in that state makes it all the more valuable. Spoiler alert: Delta B.1.617.2 is NOT YET the most common variant for vaccine breakthrough cases in Washington State! That situation will almost certainly change over the next few weeks as Delta becomes more dominant across the U.S.
The most common variant currently causing vaccine breakthroughs in Washington State up to 30th June 2021 is Alpha, (B.1.1.7), at 37%, followed by Gamma (P.1) at 17%. The Delta variant (B.1.617.2) currently only accounts for about 5% of vaccine breakthrough infections.
The Epsilon variant (B.1.429) is showing as being responsible for 15% of all breakthrough cases, yet represents just 3% of the total genome sequences for May to June, and never rose above 10% of genome samples from April 2021.
Washington State data on all breakthrough cases:
Source: Washington State Vaccine Breakthrough Report
Sars-CoV-2 variants circulating in Washington State April – June 2021:
Source: Washington Covid-19 Dashboard
As you can see, Washington State has recorded 2,228 vaccine breakthrough cases in total which represents a tiny fraction of the 6 million people now vaccinated in that state.
Our thanks to The Washington State Department of Health for providing this vital information.
USA: Washington State Vaccine Breakthroughs by Variant up to 14th July 2021
USA: Washington State Vaccine Breakthroughs by Variant up to 7th July 2021
Israel: 50% vaccine breakthrough for coronavirus cases in the last month