UK #coronavirus variant B.1.1.7 may not have evolved spontaneously in the UK or within human populations

“Here we analyzed 454,443 SARS-CoV-2 spike genes/proteins and 14,427 whole-genome sequences. We demonstrated that the early variant B.1.1.7 may not have evolved spontaneously in the United Kingdom or within human populations. Our extensive analyses suggested that Canidae, Mustelidae or Felidae, especially the Canidae family (for example, dog) could be a possible host of the direct progenitor of variant B.1.1.7.”

Biorxiv preprint: Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2

 

 

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US Congress letter to Peter Daszak requesting information concerning Wuhan Institure of Virology

US Congress letter to Peter Daszak requesting information concerning Wuhan Institure of Virology

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“Gain of Function research hasn’t protected us from this outbreak, hasn’t provided us with any effective treatments or vaccines to save hundreds of thousands of lives lost to CoV2, and if there is even a 0.1% chance GOF research caused the whole thing, that chance is too high”

Lab-Made? SARS-CoV-2 Genealogy Through the Lens of Gain-of-Function Research

CoV2 is an obvious chimera (though not nesessarily a lab-made one), which is based on the ancestral bat strain RaTG13, in which the receptor binding motif (RBM) in its spike protein is replaced by the RBM from a pangolin strain, and in addition, a small but very special stretch of 4 amino acids is inserted, which creates a furin cleavage site that, as virologists have previously established, significantly expands the “repertoire” of the virus in terms of whose cells it can penetrate.

From an investigation into the Lab Leak theory for Sars-Cov-2 By Yuri Deigin

 

 

 

 

 

WOW. Unexpected novel Merbecovirus discoveries in agricultural sequencing datasets from Wuhan, China #coronavirus

In this study we document the unexpected discovery of multiple coronaviruses and a BSL-3 pathogen in agricultural cotton and rice sequencing datasets. In particular, we have identified a novel HKU5-related Merbecovirus in a cotton dataset sequenced by the Huazhong Agricultural University in 2017.  We have also found an infectious clone sequence containing a novel HKU4-related Merbecovirus related to MERS coronavirus in a rice dataset sequenced by the Huazhong Agricultural University in early 2020. Another HKU5-related Merbecovirus, as well as Japanese encephalitis virus, were identified in a cotton dataset sequenced by the Huazhong Agricultural University in 2018. An HKU3-related Betacoronavirus was found in a Mus musculus sequencing dataset from the Wuhan Institute of Virology in 2017. Finally, a SARS-WIV1-like Betacoronavirus was found in a rice dataset sequenced by the Fujian Agriculture and Forestry University in 2017. Using the contaminating reads we have extracted from the above datasets, we were able to assemble complete genomes of two novel coronaviruses which we disclose herein. In light of our findings, we raise concerns about biosafety protocol breaches, as indicated by our discovery of multiple dangerous human pathogens in agricultural sequencing laboratories in Wuhan and Fouzou City, China.

Arxiv Preprint

 

 

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Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2 #coronavirus

In this work, we reconstruct the evolutionary events that have accompanied the emergence of SARS-CoV-2, with a special emphasis on the RBD and its adaptation for binding to its receptor, human ACE2 (hACE2). In particular, we identify a specific recombination event which involved ancestral lineages to both SARS-CoV and SARS-CoV-2. By reconstruction of ancestral states of the Spike gene, we find that this ancestral recombination event is associated with an increased binding affinity towards hACE2. Through structure-based binding affinity predictions, we infer that affinity further increased in the lineages leading to SARS-CoV and SARS-CoV-2. These observations suggest that RBD recombination provides the backbone for CoV adaptation to humans, with subsequent point mutations further permitting high affinity RBD-hACE2 binding

BiorXiv preprint

 

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Joint Statement on the WHO-Convened COVID-19 Origins Study signed by 14 countries

The text of the following statement was released by the Governments of the United States of America, Australia, Canada, Czechia, Denmark, Estonia, Israel, Japan, Latvia, Lithuania, Norway, the Republic of Korea, Slovenia, and the United Kingdom.

The Governments of Australia, Canada, Czechia, Denmark, Estonia, Israel, Japan, Latvia, Lithuania, Norway, the Republic of Korea, Slovenia, the United Kingdom, and the United States of America remain steadfast in our commitment to working with the World Health Organization (WHO), international experts who have a vital mission, and the global community to understand the origins of this pandemic in order to improve our collective global health security and response. Together, we support a transparent and independent analysis and evaluation, free from interference and undue influence, of the origins of the COVID-19 pandemic. In this regard, we join in expressing shared concerns regarding the recent WHO-convened study in China, while at the same time reinforcing the importance of working together toward the development and use of a swift, effective, transparent, science-based, and independent process for international evaluations of such outbreaks of unknown origin in the future.

The mission of the WHO is critical to advancing global health and health security, and we fully support its experts and staff and recognize their tireless work to bring an end to the COVID-19 pandemic, including understanding how the pandemic started and spread. With such an important mandate, it is equally essential that we voice our shared concerns that the international expert study on the source of the SARS-CoV-2 virus was significantly delayed and lacked access to complete, original data and samples. Scientific missions like these should be able to do their work under conditions that produce independent and objective recommendations and findings. We share these concerns not only for the benefit of learning all we can about the origins of this pandemic, but also to lay a pathway to a timely, transparent, evidence-based process for the next phase of this study as well as for the next health crises.

We note the findings and recommendations, including the need for further studies of animals to find the means of introduction into humans, and urge momentum for expert-driven phase 2 studies.  Going forward, there must now be a renewed commitment by WHO and all Member States to access, transparency, and timeliness. In a serious outbreak of an unknown pathogen with pandemic potential, a rapid, independent, expert-led, and unimpeded evaluation of the origins is critical to better prepare our people, our public health institutions, our industries, and our governments to respond successfully to such an outbreak and prevent future pandemics.  It is critical for independent experts to have full access to all pertinent human, animal, and environmental data, research, and personnel involved in the early stages of the outbreak relevant to determining how this pandemic emerged. With all data in hand, the international community may independently assess COVID-19 origins, learn valuable lessons from this pandemic, and prevent future devastating consequences from outbreaks of disease.

We underscore the need for a robust, comprehensive, and expert-led mechanism for expeditiously investigating outbreaks of unknown origin that is conducted with full and open collaboration among all stakeholders and in accordance with the principles of transparency, respect for privacy, and scientific and research integrity. We will work collaboratively and with the WHO to strengthen capacity, improve global health security, and inspire public confidence and trust in the world’s ability to detect, prepare for, and respond to future outbreaks.

Joint Statement on the WHO-Convened COVID-19 Origins Study

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WHO report on #coronavirus pandemic origins published

Arguments in favour [of a lab leak] : Although rare, laboratory accidents do happen, and different laboratories around the world are working with bat CoVs. When working in particular with virus cultures, but also with animal inoculations or clinical samples, humans could become infected in laboratories with limited biosafety, poor laboratory management practice, or following negligence. The closest known CoV RaTG13 strain (96.2%) to SARS-CoV-2 detected in bat anal swabs have been sequenced at the Wuhan Institute of Virology. The Wuhan CDC laboratory moved on 2nd December 2019 to a new location near the Huanan market. Such moves can be disruptive for the operations of any laboratory.

Arguments against [a lab leak] : The closest relatives of SARS-CoV-2 from bats and pangolin are evolutionarily distant from SARS-CoV-2. There has been speculation regarding the presence of human ACE2 receptor binding and a furin-cleavage site in SARS-CoV-2, but both have been found in animal viruses as well, and elements of the furin-cleavage site are present in RmYN02 and the new Thailand bat SARSr-CoV. There is no record of viruses closely related to SARS-CoV-2 in any laboratory before December 2019, or genomes that in combination could provide a SARS-CoV-2 genome. Regarding accidental culture, prior to December 2019, there is no evidence of circulation of SARS-CoV-2 among people globally and the surveillance programme in place was limited regarding the number of samples processed and therefore the risk of accidental culturing SARS-CoV-2 in the laboratory is extremely low. The three laboratories in Wuhan working with either CoVs diagnostics and/or CoVs isolation and vaccine development all had high quality biosafety level (BSL3 or 4) facilities that were well-managed, with a staff health monitoring programme with no reporting of COVID-19 compatible respiratory illness during the weeks/months prior to December 2019, and no serological evidence of infection in workers through SARS-CoV-2-specific serology-screening. The Wuhan CDC lab which moved on 2nd December 2019 reported no disruptions or incidents caused by the move. They also reported no storage nor laboratory activities on CoVs or other bat viruses preceding the outbreak.

WHO-convened Global Study of Origins of SARS-CoV-2

 

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WHO #coronavirus leaked report “virus most probably jumped from bats into farmed animals, before spreading to humans”

The long awaited World Health Organization report on the origins of Sars-Cov-2 has concluded that a leak from a laboratory, while possible, is “extremely unlikely”.

Instead, the virus was most likely to have been passed from bats via an “intermediate animal host” to humans before sparking an “explosive outbreak” in Wuhan in December 2019, it says.

The Telegraph has obtained a copy of the report, which has been repeatedly delayed but was sent to all WHO member states on Sunday evening.

The Telegraph report

 

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Timing the SARS-CoV-2 #coronavirus index case in Hubei province, China

“Consequently, the index case in Hubei likely contracted SARS-CoV-2 on or around 04 November 2019”.

Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province. By characterizing the likely dynamics of the virus before it was discovered, we show that over two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.

Science Mag reportTiming the SARS-CoV-2 index case in Hubei province”

 

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Dr. Peter Daszak says #coronavirus origins could be known ‘within the next few years’

The origins of the coronavirus will most likely be known within the next few years, according to a key member of a World Health Organization-led investigation into the pandemic’s origins.

“I’m convinced we are going to find out fairly soon,” Dr. Peter Daszak, a member of the WHO-led team and an animal disease specialist, said on Wednesday during a webinar hosted by think tank Chatham House.

“Within the next few years, we are going to have real significant data on where this came from and how it emerged,” he added.

CNBC report

 

 

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WHO Investigators scrap plans for interim report on probe of #coronavirus origins

WSJ:  “The World Health Organization team investigating the origins of Covid-19 is planning to scrap an interim report on its recent mission to China amid mounting tensions between Beijing and Washington over the investigation and an appeal from one international group of scientists for a new probe. A group of two dozen scientists is calling in an open letter on Thursday for a new international inquiry. They say the WHO team that last month completed a mission to Wuhan—the Chinese city where the first known cases were found—had insufficient access to adequately investigate possible sources of the new coronavirus, including whether it slipped from a laboratory.”

Open Letter Link    “Call for a Full and Unrestricted International Forensic Investigation into the Origins of COVID-19”

WSJ full report

 

 

#Coronavirus variant circulating in #Brescia, Italy since August 2020 has #501 and #493 mutation. Possible B.1.1.7 precursor.

“A variant of coronavirus circulating in Italy since early August 2020 is “very similar to the infamous English variant [B.1.1.7]”.

An ” Italian variant ” discovered in Brescia, “which precedes the variant that emerged only at the end of September in the United Kingdom and then spread to Europe, including Italy, and could also be a precursor”.

This was announced to Adnkronos Salute by Arnaldo Caruso , president of the Italian Society of Virology (Siv-Isv), full professor of Microbiology and Clinical Microbiology at the University of Brescia, director of the Asst Spedali Civili microbiology laboratory.

The variant identified, he explains, “has several points mutation in the Spike protein , the ‘hook’ that the virus uses to attack the receptor present on target cells in our body. Like the English one, the Italian variant also has a mutation in a nerve center of the Spike / cell receptor interaction, more precisely in position 501 ″.

But unlike the Gb mutant, “the Italian variant also has a second mutation in position 493, which makes its Spike protein slightly different from that of the pandemic virus we all know today”.

Calabriadirettanews.com article

 

 

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Event 201 – A pandemic exercise hosted by Johns Hopkins Center for Health Security, the World Economic Forum and the Bill and Melinda Gates Foundation on October 18, 2019, in New York, NY

Event 201 is a pandemic tabletop exercise hosted by The Johns Hopkins Center for Health Security in partnership with the World Economic Forum and the Bill and Melinda Gates Foundation on October 18, 2019, in New York, NY

#Coronavirus was already spreading in #France in late December 2019

RT-PCR was performed retrospectively on the stored respiratory sample [from December 2019] and confirmed the diagnosis of SARS-CoV-2 infection. Based on this result, it appears that the COVID-19 epidemic started much earlier in France.

Here we report a case of a patient hospitalised in December 2019 in an intensive care unit in a hospital in the north of Paris for haemoptysis with no aetiological diagnosis. RT-PCR was performed retrospectively on the stored respiratory sample and confirmed the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Based on this result, it appears that the COVID-19 epidemic started much earlier in France.

Full report

 

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