Category: Mutation
USA: Republican Mike McCaul’s final report into the origins of the Sars-CoV-2 pandemic
Mike McCaul’s final report on the origins of the pandemic can be downloaded here.
A House Republican lawmaker’s investigation into the origins of COVID-19 is raising concerns that the pandemic outbreak stemmed from a genetically modified virus which leaked from the Wuhan Institute of Virology, the Chinese city where the disease was first detected in December 2019.
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
Kit Yates on “We have to learn to live with the virus”
What do the people who say “learn to live with the virus” actually mean?
They mean: fail to learn any of the lessons of the last 18 months, fail to mitigate against the spread of the virus and tolerate avoidable deaths and disease burden.
I’d rather we didn’t.
— Kit Yates (@Kit_Yates_Maths) July 30, 2021
Over to you Kirsty….
CDC: the next variant that might emerge, just a few mutations potentially away, could eventually evade our vaccine
CDC Director Rochelle Walensky spells out what the next Sars-CoV-2 variant after Delta may be capable of
CDC Director Dr. Rochelle Walensky says “the big concern is that the next variant that might emerge, just a few mutations potentially away, could eventually evade our vaccine.”
She adds: “Right now … these vaccines operate really well in protecting us…” pic.twitter.com/QfpRhppfqS
— The Recount (@therecount) July 27, 2021
Israel: We have to learn to live with Covid
“We all need to change our thinking and draw a road map for living with Covid,” says Dr. Manfred Green. We disagree, and we will be explaining why we disagree in a post later.
Editors note: This report comes just 48 hours after our warning that Boris Johnson’s government was proposing to his countrymen that they should also “learn to live with Covid” (see original post below).
Have you ever wondered what happens when you search for “We have to learn to live with Ebola”? Try it.
It’s an idea so insane that only one person in recorded history has actually written it down.
Netherlands: the reproduction R rate is now 2.17 – the highest since February 2020
For the first time since the start of the coronavirus pandemic, people in the Netherlands infected with the SARS-CoV-2 virus were likely infecting at least two other people. The basic reproduction (R) number has swelled to an estimated 2.17, said Aura Timen of the RIVM. That estimate suggests 100 contagious people infect 217 others, who can in turn give the infection to 471 more individuals.
The new R-number is an estimate for June 30. It has only been higher on February 24, 2020 when the RIVM model put that number at an estimated 2.18, according to the Ministry of Health’s Coronavirus Dashboard.
The most recent genome sequencing results are showing the Delta variant at about 50% and increasing. There’s undoubtedly a lesson here for Boris Johnson and hos proposed unlocking of the UK in just 6 days time.
OurWorldinData.org is showing the R rate as over 3!
The Netherlands now has one of the HIGHEST R RATES EVER RECORDED in the pandemic. Below we have charted the very few countries that have had similar or higher R rates in the past.
UK: vaccine breakthroughs now nearly HALF of all new Covid-19 cases
India: Delta Plus Delta-AY.1 dominant in Tripura – found in 138 out of 151 coronavirus sequences
At least 138 of the 151 Covid-19 samples sent by Tripura for genome sequencing have tested positive for the Delta Plus variant, State Health Surveillance Officer Dr Deep Kumar Debbarma said. Tripura, thus, is the first state in the northeast to have recorded a case of the Delta Plus variant.
Addressing reporters on Friday evening, Debbarma said the samples were sent to a laboratory at Kalyani, West Bengal, for the virological test. “Delta Plus variant was found in 138 of the 151 samples. 10 others tested positive for the Delta variant while three cases of alpha variant were found,” Debbarma added.
UK: Oxford overwhelmed by Delta coronavirus variant in just 3 weeks
Covid cases in Oxford have increased fivefold in one week, almost entirely among 15 to 24-year-olds, according to the latest official figures. The number of positive cases rose from 175 to more than 899 in the seven days to 30 June – which saw the city’s fourth-highest number of daily cases. The rate (cases per 100,000 people) went up from 115 to 590 – an increase of 414% – over the same period. It now has the fifth-highest rate of coronavirus cases in England.
Preprint: Infectivity and immune escape of the new coronavirus variant of interest C.37 Lambda
“We also observed that the spike protein of the Lambda variant presented increased infectivity when compared with the spike protein of the Alpha and Gamma variants, both of them with reported increased infectivity and transmissibility. Together, our data show for the first time that mutations present in the spike protein of the Lambda variant confer escape to neutralizing antibodies and increased infectivity.”
“The evidence presented here reinforces the idea that massive vaccination campaigns in countries with high SARS-CoV-2 circulation rates must be accompanied by strict genomic surveillance aimed to rapidly identify new viral isolates carrying spike mutations as well as studies aimed to analyze the impact of these mutations in immune escape and vaccines breakthrough.”
Medrxiv preprint : Infectivity and immune escape of the new SARS-CoV-2 variant of interest Lambda
Preprint: The emergence of Sars-CoV-2 #coronavirus variant Lambda C.37 in South America
Photo by Paula Porto on Unsplash
Israel: 56% of serious coronavirus cases in hospitals are fully vaccinated
Eran Segal, a COVID expert and one of the top government advisers to the Israeli coronavirus cabinet said that while 56% of current serious COVID cases occur among fully-vaccinated individuals, the vaccine nevertheless remains the best possible protection against the disease.
Image by Richard van Liessum from Pixabay
Preprint: The emergence of Sars-CoV-2 coronavirus variant Lambda C.37 in South America
We report the emergence of a novel lineage of SARS-CoV-2 in South America, termed C.37. It presents seven nonsynonymous mutations in the Spike gene (Δ247-253, G75V, T76I, L452Q, F490S, T859N) and a deletion in the ORF1a gene (Δ3675-3677) also found in variants of concern (VOCs) Alpha, Beta, and Gamma. Initially reported in Lima, Peru, in late December 2020, it now accounts for 97% of Peruvian public genomes in April 2021. It is expanding in Chile and Argentina, and there is evidence of onward transmission in Colombia, Ecuador, Mexico, the USA, Germany, and Israel. On June 15, 2021, the World Health Organization designated C.37 as Variant of Interest (VOI) Lambda.
Full Medrxiv preprint: The Emergence of SARS-CoV-2 Variant Lambda (C.37) in South America
Preprint: Infectivity and immune escape of the new #coronavirus variant of interest C.37 Lambda
Image by Joaquín Enríquez from Pixabay
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
Delta coronavirus variant now dominant in the USA
The highly transmissible Delta variant is the most common strain of the Covid-19 virus circulating in the U.S., new data shows. An analysis of genetic sequencing data as of June 27 showed that the Delta strain, also known as B.1.617.2, now makes up about 40% of positive Covid-19 test samples.
** Outbreak.info is showing that the Delta variant has risen to about 47% in the last three weeks.
Chart courtesy of Outbreak.info