Preprint: Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

We present a detailed phylogenetic analysis of four SARS-CoV-2 lineages (B.1.627, B.1.628, B.1.631 and B.1.634) in order to investigate the possibility of virus recombination among them.

Prompted by reports of unusual genetic similarities among several Pango lineages detected mainly in North and Central America, we present a detailed phylogenetic analysis of four SARS-CoV-2 lineages (B.1.627, B.1.628, B.1.631 and B.1.634) in order to investigate the possibility of virus recombination among them. Two of these lineages, B.1.628 and B.1.631, are split into two distinct clusters (here named major and minor).

We conclude that the B.1.628 major cluster originated from a recombination event between a B.1.631 major virus and a lineage B.1.634 virus. This scenario inferred from genetic data is supported by the spatial and temporal distribution of the three lineages, which all co-circulated in the USA and Mexico during 2021, suggesting this region is where the recombination event took place. We therefore support the designation of the B.1.628 major cluster as recombinant lineage XB in the Pango nomenclature. The widespread circulation of lineage XB across multiple countries over a longer timespan than the previously designated recombinant XA lineage raises important questions regarding the role and potential effects of recombination on the evolution of SARS-CoV-2 during the ongoing COVID-19 pandemic.

 

Preprint: Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

 

Preprint: Genome recombination between Delta and Alpha variants of SARS-CoV-2

 

 

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Mexico: Patient coinfected with MU and Delta Covid variants at the same time

The governor of the state of Hidalgo, Mexico, reported that the Ministry of Health has detected the presence of COVID-19 Delta and Mu variants in the same patient.  The state president assured that it is an unprecedented event in Mexico, since the two variants had never been detected in the same case of the SARS-CoV-2 coronavirus.

The finding was confirmed by the Institute for Epidemiological Diagnosis and Reference (INDRE) of the federal Ministry of Health, as well as by a third laboratory.

 

 

 

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Ethiopia: man survives triple coinfection of Covid-19, HIV, and tuberculosis

A 55-year-old male arrived at the hospital with HIV, Covid-19 and tuberculosis. On June 6, 2021, the patient recovered and was discharged after 10 days in hospital

This case report suggests, after 10 days of admission with triple infections, there is a good clinical prognosis and survival from COVID-19. On admission, further diagnosis and investigations of TB coinfection should be performed for all patients admitted with COVID-19 due to their similar and non-specific clinical manifestations.

Dovepress.com case report

 

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WHO: Vaccines won’t save us. We’ll have to learn to live with the virus

The World Health Organization has thrown in the towel and surrendered to Covid. The WHO have finally realised that Covid-19 vaccines aren’t going to save our asses, and they are now recommending that governments around the world learn to live with the virus. Yes, that’ll be the same virus that has already killed millions, disabled tens of millions, and infected hundreds of millions. Sars-CoV-2 is apparently something we can learn to live with though, just like the ebola virus, or polio, or smallpox, or the bubonic plague.

Welcome to the new normal!

Dr Hans Kluge:  “I think it brings us to the point that the aim of a vaccination is first and foremost to prevent more serious disease, and that’s mortality. If we consider that Covid will continue to mutate and remain with us, the way influenza is, then we should anticipate how to gradually adapt our vaccination strategy to endemic transmission and gather really precious knowledge about the impact of additional jabs,” he added.

Hans Kluge quotes from The Straitstimes.com article

The Daily Mail has gone into meltdown over this one:Covid vaccines won’t end pandemic and officials must now ‘gradually adapt strategy’ to cope with inevitable spread of virus, World Health Organization official warns

 

Kirsty Allsopp: We have to learn to live with Covid

 

** Just to be clear, there will be NO mild “endemic” phase of Sars-CoV-2.  Throwing in the towel now will condemn hundreds of millions to die because we haven’t got the backbone to make the sacrifices necessary. **

 

 

USA: Texas sees coinfections with flu and Covid-19

The Nueces County Public Health District in Texas announced that the County has started seeing people who not only have COVID-19, but the flu as well. Health Director Annette Rodriguez said she got that information from a number of area doctors she has spoken with who said test results from their patients showed they had COVID-19 and the flu. “We will do something where we’re giving COVID vaccines probably at the same time that we’re giving flu vaccines,” Rodriguez said. 

Kiiitv.com report

 

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USA: more than half of COVID-19 patients at Texas Children’s Hospital also have RSV

Among 45 pediatric COVID-19 patients at Texas Children’s Hospital in Houston, at least 25 also have respiratory syncytial virus, the Houston Chronicle reported Aug. 11. More than half of the children with both illnesses have been hospitalized. About half of the hospital’s coinfected patients are infants, and most are children under 5, according to the Houston Chronicle.

Texas Children’s has also recently identified its first case of the delta plus variant, which spreads more easily than the original delta strain.

Beckershospitalreview.com

 

 

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Shi Zhengli: We need to learn to live with the virus

Shi Zhengli, China’s ‘Bat Woman’, has said that new variants of Sars-Cov-2 will continue to emerge, but that vaccines are ‘effective’.  “We shouldn’t panic, but we need to prepare to co-exist with the virus in the long term,” Shi told media on Wednesday.

Globaltimes.cn report

 

 

Dominic Minghella on “Learning to live with Covid”

This  👆  👆  👆

 

UK SAGE Bombshell Report: The Long Term Evolution of Sars-CoV-2

Scenario One: A variant that causes severe disease in a greater proportion of the population than has occurred to date.  Scenario Two: A variant that evades current vaccines.  Scenario Three: Emergence of a drug resistant variant after anti-viral strategies.  Scenario Four: SARS-CoV-2 follows an evolutionary trajectory with decreased virulence.

 

Scenario One: A variant that causes severe disease in a greater proportion of the population than has occurred to date. For example, with similar morbidity/mortality to other zoonotic coronaviruses such as SARS-CoV (~10% case fatality) or MERS-CoV (~35% case fatality).

Likelihood of increased severity phenotype: Realistic possibility.

 

Scenario Two: A variant that evades current vaccines. This could be caused by: Antigenic ‘shift’: Natural recombination events that insert a different spike gene sequence (or partial sequence) from human CoVs MERS-CoV (highly unlikely due to the low frequency of MERS-CoV infections), or from currently circulating endemic human CoVs (more likely due to the prevalence of these viruses). This would recombine into the ‘body’ of SARS-CoV-2 that is capable of high replication in human cells. The consequence could be a virus that causes disease at a level similar to COVID-19 when it first emerged but against which our current battery of spike glycoprotein-based vaccines would not work. 

Likelihood: Realistic possibility.

 

Scenario Three: Emergence of a drug resistant variant after anti-viral strategies. This could be caused by: Emergence of new variants following the administration of directly acting antiviral therapies. As we begin to use directly acting antiviral drugs it is highly likely a variant will be selected that had resistance to individual agents. For example, drugs that target the viral 3C protease, drugs that target the polymerase, monoclonal antibodies that target the spike glycoprotein. If the drugs are used as a mono therapy, then resistant variants have a high probability of emerging. This may render all drugs in that category unusable.

Likelihood: Likely – unless the drugs are used correctly.

 

Scenario Four: SARS-CoV-2 follows an evolutionary trajectory with decreased virulence. This could be caused by: Variants arising with increased transmissibility but decreased pathogenesis/virulence as the virus becomes fully adapted to the human host becoming an endemic infection. Coupled with the likelihood of eventual high populations immunity the infection produces less disease. In other words, this virus will become like other human CoV that causes common colds, but with much less severe disease predominantly in the old or clinically vulnerable. 

Likelihood: Unlikely in the short term, realistic possibility in the long term.

 

Download the entire report here

GOV.UK SAGE Website Link

 

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

Kit Yates on “We have to learn to live with the virus”

Over to you Kirsty….

Kirsty Allsopp: We have to learn to live with Covid

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.

 

We have to learn to live with Covid.

We have to learn to live with Covid.

“Learning to live with Covid” will be coming to your country soon. Be prepared.

 

Boris Johnson tells Britons to “learn to live with Covid

 

UK: Third Covid-19 wave is the worst yet

English Freedom Day: Lions led by Zombies

A short reminder of what happened after “Freedom Day” was announced in the Czech Republic on July 2nd 2020:

 

 Covid-19 cases after “Freedom Day” in the Czech Republic in 2020:

 Covid-19 deaths after “Freedom Day” in the Czech Republic in July 2020:

English Freedom Day – Lions led by Zombies.

 

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.

Eurekalert.org report

 

 

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