Category: Testing
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: 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.
Closely tracking the delta+ lineages now across the world, one of the lineages AY.3 seems to be emerging in the United States of America. This tweetorial is to summarise the observations. I will be updating this thread as new evidence emerges.
Thanks pic.twitter.com/2YtsbqmC6y— Vinod Scaria (@vinodscaria) July 24, 2021
Nextstrain makes AY.3 looks pretty widespread in the US already… pic.twitter.com/jO3hrKLRl3
— Ryan M. Ferris (@rferrisx) July 24, 2021
Github: AY.3.1 – a new sub-lineage of AY.3 concentrated in Mississippi, USA
Preprint: Emergence and spread of a B.1.1.28-derived lineage with Q675H and Q677H Spike mutations in Uruguay
In a previous study we found a sublineage B.1.1.28+Q675H+Q677H with local transmission in Rocha, a Uruguayan department bordering Brazil. This clade probably arose by early November, 2020, and its introduction from other parts of Uruguay seemed like a reasonable hypothesis. To understand whether these sequences were part of a new emergent SARS-CoV-2 lineage broadly disseminated in Uruguay, herein we analyzed the genetic diversity of B.1.1.28 SARS-CoV-2 viruses circulating in different localities by the end of 2020 and first months of 2021.
Preprint: Emergence and spread of a B.1.1.28-derived lineage with Q675H and Q677H Spike mutations in Uruguay
Image by Leandro Ubilla 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
Netherlands: 1,100 people infected with Covid-19 at superspreader test event festival
At least 130 visitors were already infected with Covid-19 despite the mandatory entrance tests when they went to the Dutch music festival ‘Verknipt’ in the first weekend of July. Afterwards, 1,100 of the 20,000 festival-goers tested positive there.
The Dutch health service points to the too long validity of the rapid tests at the time. “This research shows how vulnerable working with access tests is,” says virologist Steven Van Gucht.
Netherlands superspreader event sees one person infect 180 people in nightclub
The coronavirus outbreak at the Aspen Valley nightclub in Enschede on June 26 that resulted in 180 people contracting the coronavirus can be traced back to one person, an investigation from the GGD Twente showed. Other factors also facilitated the widespread of the disease on that night.
“There are strong indications there was one person infected with the SARS-CoV-2 coronavirus present who caused the remaining infections”, said Dr. Sanne Mensink of the GGD in a statement. Attendees were required to show proof of vaccination or negative coronavirus test upon entry.
Image by Cor Gaasbeek from Pixabay
WAPO: 35,000 symptomatic Covid-19 infections per week among 162 million vaccinated Americans
“CDC Director Rochelle Walensky privately briefed members of Congress on Thursday, drawing on much of the material in the document. One of the slides states that there is a higher risk among older age groups for hospitalization and death relative to younger people, regardless of vaccination status. Another estimates that there are 35,000 symptomatic infections per week among 162 million vaccinated Americans.”
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“vaccinated individuals infected with Delta may be able to transmit the virus as easily as those who are unvaccinated. Vaccinated people infected with Delta have measurable viral loads similar to those who are unvaccinated and infected with the variant.”
Washington Post: The War Has Changed
CDC: The Covid-19 report that changed the CDC’s view on facemasks
Image by David Mark from Pixabay
Preprint: Cryptic Sars-CoV-2 Lineages Detected in NYC Wastewater – Possible Animal Reservoir Detected
Researchers find signs of Covid-19 mutations in NYC sewage, pointing to possible dog and rat infections. After months of testing and re-testing, they found four combinations of COVID mutations that, when compared to a global database of more than 2.5 million sequenced variants, had not been seen before. The four variants are at least somewhat antibody-resistant, which could reduce the effectiveness of vaccines, the researchers found.
As with other animals, COVID-19 could be infecting dogs and rats, leading to new mutations and an outbreak in New York City’s sewers. While animal-to-human transmission of the virus is exceedingly rare, it has been seen in the U.S. in minks
These lineages contain mutations rarely observed in clinical samples, including Q493K, Q498Y, H519N and T572N. Many of these mutations were found to expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor.
MedrXiv paper: Tracking Cryptic Sars-CoV-2 Lineages Detected in NYC Wastewater
USA: Sars-CoV-2 antibodies detected in 33% of White-Tailed Deer samples
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
NEJM: Vaccine breakthrough infections leading to long Covid
Among 1497 fully vaccinated health care workers, 39 SARS-CoV-2 breakthrough infections were documented. On follow-up questioning, 31% of all infected workers reported having residual symptoms 14 days after their diagnosis. At 6 weeks after their diagnosis, 19% reported having “long Covid-19” symptoms, which included a prolonged loss of smell, persistent cough, fatigue, weakness, dyspnea, or myalgia.
Nine workers (23%) took a leave of absence from work beyond the 10 days of required quarantine; of these workers, 4 returned to work within 2 weeks. One worker had not yet returned after 6 weeks.
NEJM research article: Covid-19 Breakthrough Infections in Vaccinated Health Care Workers
See also MedrXiv preprint: Breakthrough Symptomatic COVID-19 Infections Leading to Long Covid: Report from Long Covid Facebook Group Poll
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.”
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
USA: Sars-CoV-2 antibodies detected in 33% of White-Tailed Deer samples
Antibodies to SARS-CoV-2 were detected in 33% of the 481 samples collected from January 2020 through 2021. None of the deer populations surveyed showed signs of clinical illness associated with SARS-CoV-2. Results of the study indicate that certain white-tailed deer populations in Illinois, Michigan, New York, and Pennsylvania were exposed to SARS-CoV-2.
It is important to note that this surveillance was designed to determine exposure of deer to SARS-CoV-2 in their natural environment. It was not designed to determine whether the deer were replicating and shedding SARS-CoV-2.
Image by Robert Woeger from Pixabay
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
England: Care home Covid-19 deaths double in a fortnight
Latest Care Home (CH) COVID death data (to last Friday) unfortunately shows a significant increase (doubled in a fortnight) after several low weeks.
This is a population that is ~99% fully vax'd, although staff are only around 77% fully vax'd.
— John Roberts (@john_actuary) July 27, 2021
Please check your care home lockdown plans now, this could escalate quite quickly.
Portugal: coronavirus infection rates rising fastest amongst the 80+ age group