Coronavirus Pandemic: Apocalypse Now! Or exaggerated scare story?

[Z...]

From a citizen in Elmhurst NYC:

I expect shutting down of internet is inevitable sooner than we think.
Guys how are those telepathic abilities progressing- how on earth are we going to stay in touch ?!

 

[SlipNet]

Really finding the last few days hard going. Being only able to go out once a day is getting me down, and on a few occasions I've just thought "damn it, I'm going out for a walk anyway". Spoke to my younger brother on the phone today, he's the same, really finding this too much to handle. He lives alone so he's got it even worse than me.

We had a pleasant surprise this morning though; my Auntie popped round briefly with some food supplies, she's a good soul and a Christian woman. I've got to do the whole supermarket thing again tomorrow, and with my current downer mood I'm not looking forward to it. I'm also having trouble getting to sleep, despite my meds and melatonin. I get to sleep eventually but then I sleep late which in my household is a tad problematic.

Jeez, it's only been a few weeks, I just don't know how I'm going to adjust to this lasting for months!

 

[Agron]

Last month, after I bought a school desk to hide under, Gerda assured me this would not be necessary. She’s usually right about such things, so now my defense against any microbes that might get into the house is a shotgun.

I respect Koontz. Hes a good writer and his style suits me.
Have read some of his novels... it was very long ago so I dont remember the titles at a glance, I think some SF set in future but im not sure, and I gave away the books for some reason..

Now I respect him much more and I couldnt agree more. I live alone and I cant be picky about how am I gonna reply to any wrong knock on my door. Its better to have tools for self defense, especially in the times when our sold out governments propose releasing criminals from prisons... Nevermind their obvious intentions to hook us up into their surveilance programs and take away our cash.

I have a story (and relevant for today indeed)... and seeing Koontz inspired me to write haha. btw I was into some far fetching SF and fantasy and history by writers like Neal Stephenson and Dan Simmons so my immagination knows hardly any bounds.
I had an acquaintance who went to Germany with his wife and kids, to find work and live. He sadly ended his life a long time ago now rip. To cut the long story short he was into IT and advanced comp systems. Mischievous guy by nature but also a sort of shizophrenic , I think he had to take medication. He also did drugs when he returned here for holidays couple times a year. Rampant drug/pill use among all levels of society was the norm, rahter than exception here during the 90s war. I have seen heroin and army grade amphetamin handed out for free on numerous occasions. Older guys were giving it to any inquisitive 16 and 17 year olds....
So he danced a thin line with his health and that was stated as the reason for his suicide. A fall from balcony while intoxicated. But another story was he was sort of pushed into it or was even helped, when he supposedly found out he was followed and stalked, the reason for that being that he downloaded some government documents which he then took home. Leaving his wife and kids and good paycheck behind him. I cant really remember details of him and I didnt know more more than this. I think I met him 10-20 times tops, majority of those times with bags of all kinds of illegal stuff. The 90s here were wilder than the movies. And I actually have seen one of the pictures he took. It was showing a pic of a progarm that was tracking citizens. And he explained that it can be set to warn the authorities that innapropriate human interactions are occuring. No crowds with forks or people getting together in larger numbers to conspire against papa and mama government, the literal abomination we are now lteraly suffering. That was somewhere around the year 2000...
I write all this while my white cat is snoring btw perfect lockdown scene hehehe...

 

[angelburst29]

There seems to be some Monkey-business going on in Iraq, beyond the usual nonsense that generally takes place. U.S. Military have moved out of three bases in Iraq ( near the Syrian Border ) only to consolidate/merge with two other U.S. Military bases in Iraq.

From what I see developing, Netanyahu is behind a Military Campaign to use the Defender Europe 20 exercise (30,000 US soldiers alongside 7,000 others) to enter through Iraq - to penetrate the Syrian Border and occupy Syria - then directly attack Iran?
NATO will join forces with Military Troops amassed in Afghanistan? The Pentagon and the DoD approached Trump in a March 19 meeting in the Oval Office BUT Trump did not immediately green-light the campaign.

U.S. could rethink Iran sanctions in light of coronavirus: Pompeo
U.S Secretary of State Mike Pompeo held out the possibility on Tuesday that the United States may consider easing sanctions on Iran and other nations to help fight the coronavirus epidemic but gave no concrete sign it plans to do so.

Rouhani: U.S. has lost opportunity to lift Iran sanctions amid coronavirus
Iran's president said on Wednesday that, with the advent of the coronavirus, the United States had missed a historic opportunity to lift sanctions on his country, though the penalties had not hampered its fight against the infection.

Trump warns Iran, proxies against attacking U.S. in Iraq
U.S. President Donald Trump on Wednesday warned Iran and its proxies against attacking U.S. troops or assets in Iraq, citing a possible "sneak attack" but giving no other details.

Israeli military will continue foreign operations despite coronavirus outbreak: MoD
Bennett’s comments came a day after the Israeli Defense Forces (IDF) carried out a powerful attack on the Shayrat Airbase in the eastern countryside of Syria’s Homs Governorate.

A local military source said that Israeli planes launched a series of missiles from Lebanese airspace, and that the Syrian air defenses intercepted many of them.

The source added: “The Israeli aggression took place on one of the military headquarters in Homs countryside, and came in two waves, the first with 8 missiles, and the second with 4 missiles, and work is currently being done to limit the damage.”

Iranian official warns US against 'new military error' after Patriot missile deployment in Iraq
Abdullahian wrote on Twitter that “the re-positioning and moves of the American military in Iraq and the region might be a kind of psychological warfare.”

The possibility of attacks by the U.S. forces against Hashd Al-Sha’abi has increased recently after the international coalition evacuated bases in Iraq. Washington removed its “non-essential” employees from its embassy in Baghdad, and its consulate in Erbil, as it appears they are bracing for a new conflict.

Also, the U.S. on Monday deployed a Patriot air defense missile system at the ‘Ayn Al-Assad Base, where the American soldiers are deployed, and and another installation in Erbil, the capital of the Iraqi Kurdistan region.

“The Americans, by focusing on psychological warfare, somewhat want to advance their actions, and in this area, they launch threats against the resistance factions in Iraq and sometimes some threats to Iran,” Gawani added.

Russian plane with coronavirus medical gear flies to U.S. after Trump-Putin call

Russia is sending the United States medical equipment to help fight the coronavirus pandemic, a public relations coup for Russian President Vladimir Putin after he discussed the crisis with U.S. President Donald Trump.

 

[cassandra]

During nights since the beginning of this crapulous situation I sweat so much that my t-shirt is all wet. I don't have fever. But maybe during the night? Very strange. And that every night.

Perhaps a good way to detox also? My body was cool and in seconds I was literally gushing sweat. Is this normal?

Also, I had a kind of conversation with a lady blackbird. I put a bowl out every day full of raisins, this morning I put it on the other side, as I wanted to enjoy the sun, and not scare the birds.
She hopped on the ledge, puzzled. Now, this bowl was blocked from her view by a shrub. I telepathically sent her the message that the bowl was on the other side and nodded in the direction of the bowl. She immediately flew towards the bowl and began to eat. I think animals are telepathic, but I sense she understood the nod also.

 

[mARTinSky]

Russia is sending the United States medical equipment to help fight the coronavirus pandemic, a public relations coup for Russian President Vladimir Putin after he discussed the crisis with U.S. President Donald Trump.

Pure speculation on my side but based on strong feeling: there's more than medical equipment on this plane. Russians may be sending their medical personnel there as they did so with Italy. If so, something fishy is going on here but I may be dead wrong.

 

[biuta]

I expect shutting down of internet is inevitable sooner than we think.
Guys how are those telepathic abilities progressing- how on earth are we going to stay in touch ?!

I doubt it. As I said before, they need it in order to push people's buttons. They will simply start to filter things and shut them down as fake news, but internet will stay up in my opinion.

 

[Agron]

Excellent observation Debra. About how there are many among us who lack these basic traits that are inherent to human beings with a soul. But not all... otherwise we would already be matrixD ... gotta see the positive side aswell right!
So I would add some perspective to your thinking. If we take into account that this is a time of cleaning and healing, which some Astrologers suggest, than it is obvious how people that are truly suffering are first to either seek true salvation from their problems, or call it quits with their destructive actions, sorry for my harsh language... Im an "easterner" and sometimes I sound like Russian when I speak English hahahah... it takes some practice to sound like John Wayne
And if we believe that as soon as they die they go to the recycling area and there some of them can be of help to us. So I suggest that If you want you pray to your ancestors for guidance and see if it works ... keep at it too. As Laura suggests..

Discipline is the only way you can recognize human from monkey really... and we all take on as much as we can but this could be the time, again, Im confirming my ideas with Astrology, to take on some more

Ive found this great informative usefull thread that was started by @Joe that can be of help to anyone who needs tips and reassurance.

To quote his impressive post (I thout it wouldb be good to enlarge it)(:

Negative Emotions, Thoughts And How to Counteract Them

Here's something I came across from J G Bennett from one of his London meetings in 1972. Could be a quote from Gurdjieff, not sure. Seems like the right approach to me. "To replace all negative attitudes toward the existing world by a feeling of confidence and love toward the new world which...

cassiopaea.org

I also found this nice piece of little sets of rules and reccomendations for developing more compassion and empathy in a nice post (not sure about the links but the text lays out the basics in a nice way) and maybe pieces of it could be usefull when youre interacting with family or neighbors... which can be at times very stressfull, Ive had em. but also very rewarding. amazingly Ive had atleast 3 of those with complete strangers in last 9 days. serene, intelligent, insightfull and pleasent interactions that lasted over 10 minutes and longer.

Develop Your Spiritual Resources | Taking Charge of Your Wellbeing

Nurturing and developing your spirituality may be just as important as eating a healthy diet, exercising, and building strong relationships. Taking the time to reconnect with what you find meaningful in life and returning to life’s big questions can enhance your own sense of connection with...

www.takingcharge.csh.umn.edu

Hope this will be helpfull as it is to me and my little bunch of good people, THANK GOD!!!

Regards

Agron

Dunno why I said a different name, must have been from all this reading, sry bout that mixup @loreta ... silly me

 

[Aeneas]

And a few choice things from Twitter:

- US farmers saying they can't slaughter animals because meat processors are shut. They're being advised to sell the cattle. He expects the situation to worsen
- Meanwhile apparently US farmers and staff harvesting leaf vegetables are fine

Thank you for bringing that up. It is going to be a massive problem on the food side if the corona circus shutdown continues for much longer which it probably will.
I found another abattoir (Canadian) which is closing down for 14 days.

-So some farmers can't get their animals slaughtered,
-vegetable growers and other labour intensive agriculture businesses have problems finding people to do the work,
-the fishing industry is drastically reduced as they have difficulty getting the fish processed.

The above are all manmade problems due to the designed panic virus, which reminds me about another huge social engineering experiment with disastrous consequences which was the collectivisation under the Bolsheviks in the Soviet Union.

Lobaczewski highlight this problem when psychopaths rule:

Economic factors

constitute a non-negligible part of the motivation
for this expansionist tendency. Since the managerial
functions have been taken over by individuals with mediocre
intelligence and pathological character traits, the pathocracy
becomes incapable of properly administering anything at all.
The area suffering most severely must always be whichever
one requires a person to act independently, not wasting time
searching for the proper way to behave. Agriculture is dependent
upon changing climate conditions and the appearance of
pests and plant diseases. A farmer’s personal qualities have
thus been an essential factor of success in this area, as it was
for many centuries. Pathocracy therefore invariably brings
about food shortages.

This might be another place where hubris and wishful thinking is their downfall.

Then we have climate change and quite cold weather for this time of year in Europe and North America, frost in some places which have destroyed some flowering fruit trees and therefore reduced the crops. If another wet and cold start to the planting season happens in the US like last year, then food shortages could well be a factor especially if one adds the problems of the processing of animals.

 

[Revolucionar]

I need to find a large heap of cow manure to start my no dig garden (gotta prepare for them food riots), but I can't just go knocking on neighbours' doors. Gonna get reported as a rule breaker. Damn fascist lockdown, getting in the way of my survival plans.

 

[bianca etezete]

The BBC reports that the banks, appointed by the government via a pot of £330 billion intended for loans to small businesses during the lock down, aren't approving at least 1/5, reflecting other stats that between 800,000 and a million firms nationwide may soon have to close. Some small business owners are being asked to secure their houses against the loans, others are being offered a 30% interest rate.

So the banks are not only benefiting from having the bail out money, they're profiting from the loans and are able to take ownership of the properties if (when) the small business is unable to pay.

Unsurprisingly, an unprecedented 950,000 people in the UK applied for state benefits (Universal Credit) between 16th-31st March - only about 100,000 have been processed.

The UK is also 'considering' dropping the move to increase the minimum wage, and it is stopping free school meals to infants - meaning children will go hungry.

Considering the above, it could get nasty.

And a few choice things from Twitter:

- US farmers saying they can't slaughter animals because meat processors are shut. They're being advised to sell the cattle. He expects the situation to worsen
- Meanwhile apparently US farmers and staff harvesting leaf vegetables are fine
- UK mosque brings in own cold storage unit to process Muslims that have died, expecting an influx and wishing to preserve their burial traditions
- In India due to work stoppage, workers from the country are stuck in the city with no money, some going back to their villages
- the Empire State Building becomes the Eye of Sauron during lockdown, apparently?

Here in Germany they said today tha already 470 000 businesses are in shorttime work. 470 000! Already. If you say that each business is only 5 to 7 persons working there (and I think that is a very low estimate) that will put more that 2.5 million peeps on short time work. Wow. The highest we ever had in short time work at one time was I think 1.4 million.

 

[cassandra]

I'm way behind on this thread, but I thought I would post the new directive, by our Health Minister this morning...

“It’s more and more [unlikely] that we’re going to be able to get back to full normal life — which I miss a lot — before at least the summer, and then we need to start preparing ourselves for the potential of a second wave in the fall,” she said.


Yeah, they seem to be the new Führer. Seem to have unlimited powers.

Yes, wasn't Brave New World run by science? I notice it and 1984 has been taken off the school syllabus for some time now.

 

[Gaby]

Here is the paper that made similarities between COVID-19 and HIV, and which was retracted and now reads:

This paper has been withdrawn by its authors. They intend to revise it in response to comments received from the research community on their technical approach and their interpretation of the results. If you have any questions, please contact the corresponding author.

Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag

We are currently witnessing a major epidemic caused by the 2019 novel coronavirus (2019-nCoV). The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid...

www.biorxiv.org

We are currently witnessing a major epidemic caused by the 2019 novel coronavirus (2019-nCoV). The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV-1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute the receptor binding site. The finding of 4 unique inserts in the 2019-nCoV, all of which have identity /similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be fortuitous in nature. This work provides yet unknown insights on 2019-nCoV and sheds light on the evolution and pathogenicity of this virus with important implications for diagnosis of this virus.

Introduction
Coronaviruses (CoV) are single-stranded positive-sense RNA viruses that infect animals and humans. These are classified into 4 genera based on their host specificity: Alphacoronavirus, Betacoronavirus, Deltacoronavirus and Gammacoronavirus (Snijder et al., 2006). There are seven known types of CoVs that includes 229E and NL63 (Genus Alphacoronavirus), OC43, HKU1, MERS and SARS (Genus Betacoronavirus). While 229E, NL63, OC43, and HKU1 commonly infect humans, the SARS and MERS outbreak in 2002 and 2012 respectively occurred when the virus crossed-over from animals to humans causing significant mortality (J. Chan et al., n.d.; J. F. W. Chan et al., 2015). In December 2019, another outbreak of coronavirus was reported from Wuhan, China that also transmitted from animals to humans. This new virus has been temporarily termed as 2019-novel Coronavirus (2019-nCoV) by the World Health Organization (WHO) (J. F.-W. Chan et al., 2020; Zhu et al., 2020). While there are several hypotheses about the origin of 2019-nCoV, the source of this ongoing outbreak remains elusive.

The transmission patterns of 2019-nCoV is similar to patterns of transmission documented in the previous outbreaks including by bodily or aerosol contact with persons infected with the virus. Cases of mild to severe illness, and death from the infection have been reported from Wuhan. This outbreak has spread rapidly distant nations including France, Australia and USA among others. The number of cases within and outside China are increasing steeply. Our current understanding is limited to the virus genome sequences and modest epidemiological and clinical data. Comprehensive analysis of the available 2019-nCoV sequences may provide important clues that may help advance our current understanding to manage the ongoing outbreak.

The spike glycoprotein (S) of cornonavirus is cleaved into two subunits (S1 and S2). The S1 subunit helps in receptor binding and the S2 subunit facilitates membrane fusion (Bosch et al., 2003; Li, 2016). The spike glycoproteins of coronoviruses are important determinants of tissue tropism and host range. In addition the spike glycoproteins are critical targets for vaccine development (Du et al., 2013). For this reason, the spike proteins represent the most extensively studied among coronaviruses. We therefore sought to investigate the spike glycoprotein of the 2019-nCoV to understand its evolution, novel features sequence and structural features using computational tools.

Methodology
Retrieval and alignment of nucleic acid and protein sequences
We retrieved all the available coronavirus sequences (n=55) from NCBI viral genome database (National Center for Biotechnology Information) and we used the GISAID (Elbe & Buckland-Merrett, 2017)[GISAID - Global Initiative on Sharing All Influenza Data] to retrieve all available full-length sequences (n=28) of 2019-nCoV as on 27 Jan 2020. Multiple sequence alignment of all coronavirus genomes was performed by using MUSCLE software (Edgar, 2004) based on neighbour joining method. Out of 55 coronavirus genome 32 representative genomes of all category were used for phylogenetic tree development using MEGAX software (Kumar et al., 2018). The closest relative was found to be SARS CoV. The glycoprotein region of SARS CoV and 2019-nCoV were aligned and visualized using Multalin software (Corpet, 1988). The identified amino acid and nucleotide sequence were aligned with whole viral genome database using BLASTp and BLASTn. The conservation of the nucleotide and amino acid motifs in 28 clinical variants of 2019-nCoV genome were presented by performing multiple sequence alignment using MEGAX software. The three dimensional structure of 2019-nCoV glycoprotein was generated by using SWISS-MODEL online server (Biasini et al., 2014) and the structure was marked and visualized by using PyMol (DeLano, 2002).


Results
Uncanny similarity of novel inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag
Our phylogentic tree of full-length coronaviruses suggests that 2019-nCoV is closely related to SARS CoV [Fig1]. In addition, other recent studies have linked the 2019-nCoV to SARS CoV. We therefore compared the spike glycoprotein sequences of the 2019-nCoV to that of the SARS CoV (NCBI Accession number: AY390556.1). On careful examination of the sequence alignment we found that the 2019-nCoV spike glycoprotein contains 4 insertions [Fig.2]. To further investigate if these inserts are present in any other corona virus, we performed a multiple sequence alignment of the spike glycoprotein amino acid sequences of all available coronaviruses (n=55) [refer Table S.File1] in NCBI refseq (ncbi.nlm.nih.gov) this includes one sequence of 2019-nCoV[Fig.S1]. We found that these 4 insertions [inserts 1, 2, 3 and 4] are unique to 2019-nCoV and are not present in other coronaviruses analyzed. Another group from China had documented three insertions comparing fewer spike glycoprotein sequences of coronaviruses. Another group from China had documented three insertions comparing fewer spike glycoprotein sequences of coronaviruses (Zhou et al., 2020).

We then analyzed all available full-length sequences (n=28) of 2019-nCoV in GISAID (Elbe & Buckland-Merrett, 2017) as on January 27, 2020 for the presence of these inserts. As most of these sequences are not annotated, we compared the nucleotide sequences of the spike glycoprotein of all available 2019-nCoV sequences using BLASTp. Interestingly, all the 4 insertions were absolutely (100%) conserved in all the available 2019-nCoV sequences analyzed [Fig.S2, Fig.S3].

We then translated the aligned genome and found that these inserts are present in all Wuhan 2019-nCoV viruses except the 2019-nCoV virus of Bat as a host [Fig.S4]. Intrigued by the 4 highly conserved inserts unique to 2019-nCoV we wanted to understand their origin. For this purpose, we used the 2019-nCoV local alignment with each insert as query against all virus genomes and considered hits with 100% sequence coverage. Surprisingly, each of the four inserts aligned with short segments of the Human immunodeficiency Virus-1 (HIV-1) proteins. The amino acid positions of the inserts in 2019-nCoV and the corresponding residues in HIV-1 gp120 and HIV-1 Gag are shown in Table 1. The first 3 inserts (insert 1,2 and 3) aligned to short segments of amino acid residues in HIV-1 gp120. The insert 4 aligned to HIV-1 Gag. The insert 1 (6 amino acid residues) and insert 2 (6 amino acid residues) in the spike glycoprotein of 2019-nCoV are 100% identical to the residues mapped to HIV-1 gp120. The insert 3 (12 amino acid residues) in 2019-nCoV maps to HIV-1 gp120 with gaps [see Table 1]. The insert 4 (8 amino acid residues) maps to HIV-1 Gag with gaps.

Although, the 4 inserts represent discontiguous short stretches of amino acids in spike glycoprotein of 2019-nCoV, the fact that all three of them share amino acid identity or similarity with HIV-1 gp120 and HIV-1 Gag (among all annotated virus proteins) suggests that this is not a random fortuitous finding. In other words, one may sporadically expect a fortuitous match for a stretch of 6-12 contiguous amino acid residues in an unrelated protein. However, it is unlikely that all 4 inserts in the 2019-nCoV spike glycoprotein fortuitously match with 2 key structural proteins of an unrelated virus (HIV-1).
The amino acid residues of inserts 1, 2 and 3 of 2019-nCoV spike glycoprotein that mapped to HIV-1 were a part of the V4, V5 and V1 domains respectively in gp120 [Table 1]. Since the 2019-nCoV inserts mapped to variable regions of HIV-1, they were not ubiquitous in HIV-1 gp120, but were limited to selected sequences of HIV-1 [refer S.File1] primarily from Asia and Africa.
The HIV-1 Gag protein enables interaction of virus with negatively charged host surface (Murakami, 2008) and a high positive charge on the Gag protein is a key feature for the host-virus interaction. On analyzing the pI values for each of the 4 inserts in 2019-nCoV and the corresponding stretches of amino acid residues from HIV-1 proteins we found that a) the pI values were very similar for each pair analyzed b) most of these pI values were 10±2 [Refer Table 1]. Of note, despite the gaps in inserts 3 and 4 the pI values were comparable. This uniformity in the pI values for all the 4 inserts merits further investigation.
As none of these 4 inserts are present in any other coronavirus, the genomic region encoding these inserts represent ideal candidates for designing primers that can distinguish 2019-nCoV from other coronaviruses.
The novel inserts are part of the receptor binding site of 2019-nCoV
To get structural insights and to understand the role of these insertions in 2019-nCoV glycoprotein, we modelled its structure based on available structure of SARS spike glycoprotein (PDB: 6ACD.1.A). The comparison of the modelled structure reveals that although inserts 1,2 and 3 are at non-contiguous locations in the protein primary sequence, they fold to constitute the part of glycoprotein binding site that recognizes the host receptor (Kirchdoerfer et al., 2016) (Figure 4). The insert 1 corresponds to the NTD (N-terminal domain) and the inserts 2 and 3 correspond to the CTD (C-terminal domain) of the S1 subunit in the 2019-nCoV spike glycoprotein. The insert 4 is at the junction of the SD1 (sub domain 1) and SD2 (sub domain 2) of the S1 subunit (Ou et al., 2017). We speculate, that these insertions provide additional flexibility to the glycoprotein binding site by forming a hydrophilic loop in the protein structure that may facilitate or enhance virus-host interactions.
Evolutionary Analysis of 2019-nCoV
It has been speculated that 2019-nCoV is a variant of Coronavirus derived from an animal source which got transmitted to humans. Considering the change of specificity for host, we decided to study the sequences of spike glycoprotein (S protein) of the virus. S proteins are surface proteins that help the virus in host recognition and attachment. Thus, a change in these proteins can be reflected as a change of host specificity of the virus. To know the alterations in S protein gene of 2019-nCoV and its consequences in structural re-arrangements we performed in-sillico analysis of 2019-nCoV with respect to all other viruses. A multiple sequence alignment between the S protein amino acid sequences of 2019-nCoV, Bat-SARS-Like, SARS-GZ02 and MERS revealed that S protein has evolved with closest significant diversity from the SARS-GZ02 (Figure 1).

Insertions in Spike protein region of 2019-nCoV
Since the S protein of 2019-nCoV shares closest ancestry with SARS GZ02, the sequence coding for spike proteins of these two viruses were compared using MultiAlin software. We found four new insertions in the protein of 2019-nCoV- “GTNGTKR” (IS1), “HKNNKS” (IS2), “GDSSSG” (IS3) and “QTNSPRRA” (IS4) (Figure 2). To our surprise, these sequence insertions were not only absent in S protein of SARS but were also not observed in any other member of the Coronaviridae family (Supplementary figure). This is startling as it is quite unlikely for a virus to have acquired such unique insertions naturally in a short duration of time.

Insertions share similarity to HIV
The insertions were observed to be present in all the genomic sequences of 2019-nCoV virus available from the recent clinical isolates (Supplementary Figure 1). To know the source of these insertions in 2019-nCoV a local alignment was done with BLASTp using these insertions as query with all virus genome. Unexpectedly, all the insertions got aligned with Human immunodeficiency Virus-1 (HIV-1). Further analysis revealed that aligned sequences of HIV-1 with 2019-nCoV were derived from surface glycoprotein gp120 (amino acid sequence positions: 404-409, 462-467, 136-150) and from Gag protein (366-384 amino acid) (Table 1). Gag protein of HIV is involved in host membrane binding, packaging of the virus and for the formation of virus-like particles. Gp120 plays crucial role in recognizing the host cell by binding to the primary receptor CD4.This binding induces structural rearrangements in GP120, creating a high affinity binding site for a chemokine co-receptor like CXCR4 and/or CCR5.

Discussion
The current outbreak of 2019-nCoV warrants a thorough investigation and understanding of its ability to infect human beings. Keeping in mind that there has been a clear change in the preference of host from previous coronaviruses to this virus, we studied the change in spike protein between 2019-nCoV and other viruses. We found four new insertions in the S protein of 2019-nCoV when compared to its nearest relative, SARS CoV. The genome sequence from the recent 28 clinical isolates showed that the sequence coding for these insertions are conserved amongst all these isolates. This indicates that these insertions have been preferably acquired by the 2019-nCoV, providing it with additional survival and infectivity advantage. Delving deeper we found that these insertions were similar to HIV-1. Our results highlight an astonishing relation between the gp120 and Gag protein of HIV, with 2019-nCoV spike glycoprotein. These proteins are critical for the viruses to identify and latch on to their host cells and for viral assembly (Beniac et al., 2006). Since surface proteins are responsible for host tropism, changes in these proteins imply a change in host specificity of the virus. According to reports from China, there has been a gain of host specificity in case 2019-nCoV as the virus was originally known to infect animals and not humans but after the mutations, it has gained tropism to humans as well.
Moving ahead, 3D modelling of the protein structure displayed that these insertions are present at the binding site of 2019-nCoV. Due to the presence of gp120 motifs in 2019-nCoV spike glycoprotein at its binding domain, we propose that these motif insertions could have provided an enhanced affinity towards host cell receptors. Further, this structural change might have also increased the range of host cells that 2019-nCoV can infect. To the best of our knowledge, the function of these motifs is still not clear in HIV and need to be explored. The exchange of genetic material among the viruses is well known and such critical exchange highlights the risk and the need to investigate the relations between seemingly unrelated virus families.

Conclusions
Our analysis of the spike glycoprotein of 2019-nCoV revealed several interesting findings: First, we identified 4 unique inserts in the 2019-nCoV spike glycoprotein that are not present in any other coronavirus reported till date. To our surprise, all the 4 inserts in the 2019-nCoV mapped to short segments of amino acids in the HIV-1 gp120 and Gag among all annotated virus proteins in the NCBI database. This uncanny similarity of novel inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag is unlikely to be fortuitous. Further, 3D modelling suggests that atleast 3 of the unique inserts which are non-contiguous in the primary protein sequence of the 2019-nCoV spike glycoprotein converge to constitute the key components of the receptor binding site. Of note, all the 4 inserts have pI values of around 10 that may facilitate virus-host interactions. Taken together, our findings suggest unconventional evolution of 2019-nCoV that warrants further investigation. Our work highlights novel evolutionary aspects of the 2019-nCoV and has implications on the pathogenesis and diagnosis of this virus.

 

[Channa]

Bonjour à tous, je pensais mettre ce texte à la dernière session des Cassiopéens mais je vois que vous parlez ici des troupes américaines.
Je joins une partie du texte que j'ai lu aujourd'hui dans une session française d'astrologie mondiale parlant de "l'invasion" des soldats américains en Europe.
Que se passe-t-il ici? J'aimerais avoir votre avis
Tendresse à vous tous

 

[Gaby]

Here's another paper that is lined up to be retracted due to criticisms, it's still up though.

On the origin and continuing evolution of SARS-CoV-2

Abstract. The SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China, and has since impacted a large portion of China and raised major global co

academic.oup.com

The SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China, and has since impacted a large portion of China and raised major global concern. Herein, we investigated the extent of molecular divergence between SARS-CoV-2 and other related coronaviruses. Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by mutations and natural selection besides recombination. Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Although the L type (∼70%) is more prevalent than the S type (∼30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure. These findings strongly support an urgent need for further immediate, comprehensive studies that combine genomic data, epidemiological data, and chart records of the clinical symptoms of patients with coronavirus disease 2019 (COVID-19).

And more basic info:

Why does the coronavirus spread so easily between people?

Researchers have identified microscopic features that could make the pathogen more infectious than the SARS virus — and serve as drug targets.

www.nature.com

Spiky invader

To infect a cell, coronaviruses use a ‘spike’ protein that binds to the cell membrane, a process that's activated by specific cell enzymes. Genomic analyses of the new coronavirus have revealed that its spike protein differs from those of close relatives, and suggest that the protein has a site on it which is activated by a host-cell enzyme called furin.

This is significant because furin is found in lots of human tissues, including the lungs, liver and small intestines, which means that the virus has the potential to attack multiple organs, says Li Hua, a structural biologist at Huazhong University of Science and Technology in Wuhan, China, where the outbreak began. The finding could explain some of the symptoms observed in people with the coronavirus, such as liver failure, says Li, who co-authored a genetic analysis of the virus that was posted on the ChinaXiv preprint server on 23 February2. SARS and other coronaviruses in the same genus as the new virus don't have furin activation sites, he says.

The furin activation site “sets the virus up very differently to SARS in terms of its entry into cells, and possibly affects virus stability and hence transmission”, says Gary Whittaker, a virologist at Cornell University in Ithaca, New York. His team published another structural analysis of the coronavirus’s spike protein on bioRxiv on 18 February3.

Several other groups have also identified the activation site as possibly enabling the virus to spread efficiently between humans4. They note that these sites are also found in other viruses that spread easily between people, including severe strains of the influenza virus. On these viruses, the activation site is found on a protein called haemagglutinin, not on the spike protein.