π¦ OMICRON - New South African Strain Of SARS-CoV-2 - CORONAVIRUS - EVERYTHING YOU NEED TO KNOW- LIVE UPDATES)
B.1.1.529
Watch the video above to learn more about this new variant OMICRON ππ»
LIVE UPDATES:
Updated last on 11/28/21 9:37 PM
On November 26th 2021 the World Health Organization classified OMICRON B.1.1.529 as new strain of SARS-CoV-2 and shortly after listed it as a VOC (Variant of Concern) as a consequence of the WHOβs TAG-VEβs (Technical Advisory Group on SARS-CoV-2 Evolutionβs) investigation. This publication will explain EVERYTHING YOU NEED TO KNOW about the new South African variant named OMICRON. Now, to be more precise, this publication will answer 4οΈβ£ important questions, then will over what you should do about the information you read. Letβs begin by looking at the four questions. π First, how is this variant different? π Second, is this variant more transmissible? π Third, is this variant evading the human immune response making immunity from vaccination or natural infection less protective - is it reducing effectiveness of monoclonal antibodies? π Fourth, are symptoms more severe compared to other variants (Delta, Beta, Alpha etcβ¦)?
π‘ To set the stage for the 4 previously mentioned questions, the facts need to be laid out first. So start here :
ππ» OMICRON B.1.1.529 was FIRST discovered and genotyped in the country BOTSWANA, a province just north of South Africa on 11/11/21, specimen was collected on 11/9/21 - so far 6 people have tested positive in Botswana
ππ» OMICRON has also been subsequently found/genotyped in Netherlands, Denmark, Canada, Hong Kong, Belgium, Israel, United Kingdom, Germany, Czech Republic, Australia, Italy
ππ» Most confirmed cases were found in Gauteng (90%), a province in South Africa
ππ» 77 confirmed cases in South Africa
ππ» Currently affecting younger men under 40 years old
ππ» Recurring symptoms: headache, extreme fatigue, body aches
ππ» ISRAEL: 1 individual that returned to Israel from Malawi in South Eastern Africa tested positive for the new variant. Also, two other cases were confirmed in Israel soon after - all individuals fully vaccinated - totaling 3 cases
ππ» BELGIUM: 1 individual that returned from Egypt tested positive for the new variant on November 11th, 2021
ππ» Hong Kong: 1 individual that came from South Africa tested positive in Hong Kong, this individual infected a neighbor that soon after tested positive for the new variant
ππ» DUTCH confirm 13 new cases 11/28/21
ππ» There is worry OMICRON B.1.1.529 may outcompete DELTA VARIANT and become the dominant strain in South Africa (or else where) considering how fast cases have jumped in such a short period of time
ππ» Africa is 6% vaccinated overall
ππ» South Africa is around 24% vaccinated
ππ» Travel ban from South Africa to USA begins Monday 11/29/21 affecting BOTSWANA, ZIMBABWE, NAMIBIA, LESOTHO, ESWATINI, MOZAMBIQUE, AND MALAWI
ππ» On Friday 11/26/21 Israel imposed a travel ban that inhibits travel from most African nations
ππ» Hong Kong, Singapore, Malaysia, Philippines, and Japan have also imposed travel ban from most African nations
ππ» New variant possibly came from someone with weakened immune system (e.g. person with untreated HIV/AIDS), as a result, some of the virus evaded host antibodies. Surviving virus then evolved from low host defenses. So this continued process of evading then evolving eventually produced enough mutated viral load to spread to the next person. So on and so forth
Now that youβve read all that, letβs look at question number 1 (continue belowππ»).
1οΈβ£ How is this variant different?
OMICRON B.1.1.529 genome sequencing revealed a few key differences. First and foremost, there were a total of about 50 mutations. To elaborate 30 of those 50 mutations were seen in the spike protein. Even more interesting, 15 of those 30 mutations were seen in the RBD (receptor binding domain) of the spike protein. To explain, there are many little spikes on the outside of the SARS-CoV-2 virus, hence the name spike protein. Well, those proteins, particularly the S1 segments, include whats called an RBD (receptor binding domain) which attaches to receptors on human cells called ACE2. Well, 10 changes in the RBD portion of the spike protein allow it to attach to host cells easier.
The group of these 4 mutations here β‘οΈ 1.) K417N, 2.) S477N, 3.)Q498R, 4.)N501Y, COUPLED WITH singular mutations here β‘οΈ Q339D, S371L, S373P, S375F, COULD HELP THE VIRUS AVOID ANTIBODIES, AND ALSO PREVENT ANTIBODIES FROM RECOGNIZING THE VIRUS, THUS OPENING THE DOOR FOR RE-INFECTION.
OMICRON on certain PCR tests exhibited S GENE DROPOUT/GENE TARGET FAILURE (explained differently, that means when tested, the S gene was absent). Importantly, the variantβs strange presentation on PCR tests could be used as a confirmation marker to confirm positivity along with genomic testing. S gene dropout is happening because of deletions at positions 69 & 70 in the virus.
Three mutations around the furin cleavage site (named PRRAR) near H655Y, N679K, and P681H could possibly increase transmissibility. Hereβs why. Furin is a protease that plays a role in cleaving/cutting envelope glycoproteins which are important to help fuse the virus with host membrane. Essentially, furin cleavage allows the virus to dock on cells easier, that way infection can continue.
Three non-spike deletions at positions 1.) L105, 2.) S106, and G107 inside of NSP6 (non-structural protein 6) could also help SARS-CoV-2 avoid the human immune system. It should be said that deletions are changes to the viral code that ultimately change the way proteins are produced and even act. That confuses host cells, and as a result increases immune evasion.
*SEE PICTURES BELOW
2οΈβ£ Is this variant more transmissible?
According to the data laid out in the previous paragraphs and pictures above, Yes it could be. It seemβs that mutations near the furin cleavage site on the spike protein at H655Y, N679K, and P681H could enable the virus to be more infectious therefore more spreadable as new attachment strategies have been adopted by the virus because of changes in its code (mutations/changes also listed below). Summed up, ENHANCED VIRAL ENVELOPE FUSION to host cells could occur, resulting in high viral load that may increase exponentially as the immune system tries to keep up with the viruses new attachment tactics. The result, the increased possibility of transmission.
3οΈβ£ Is this variant evading the human immune response making immunity from vaccination or natural infection less protective - is it reducing effectiveness of monoclonal antibodies?
Yes, and it may get worse. There is a probability of this occurring on a large scale for 3 reasons. First, a specific combination of 3 mutations 1.)K417N, 2.) S477N, 3.) Q498R coupled with these 4 separate mutations 1.) Q339D, 2.) S371L, 3.) S373P, 4.) S375F gives the virus a function which enables it to evade current host antibodies from either previous infection, vaccination or even monoclonal antibody treatment. Moreover, deletions at L105, S106, and G107 in NSP6 (not in spike protein) make it more difficult for the body to recognize this variant as those deletions were previously used by the body to recognize viral proteins and destroy invading cells. Essentially, itβs a lot of change for host cells to FIND, DEAL WITH, THEN PRODUCE NEW IMMUNITY AGAINST ALL THESE VIRAL CHANGES. Finally, breakthrough infections of this new variant have been seen in people who received vaccines from Johnson & Johnson, Pfizer, and Oxford-AstraZeneca. All and all, itβs the sum total of change in this variant thats problematic. Currently, there are 3 pieces of good news. The first piece, if you look at the graph below, show that cases seem to be reducing. Second piece of good news, increasing/boosting vaccine effectiveness against OMICRON is easy. Itβs as simple as inserting a new code into the mRNA vaccine - that applies only to Modern and Pfizer, not Johnson & Johnson which is a viral vector vaccine and not programable in the same way. Third and finally, the same upgrade can be given to monoclonal antibodies to boost effectiveness against this new variant if need be.
4οΈβ£ Are symptoms more severe compared to other variants? (Delta, Beta, Alpha etc..)?
Reportedly, severity of symptoms has not increased. Of course patients are experiencing expected side effects like shortness of breath, loss of taste/smell, nausea, vomiting, fatigue, headache, fever, chills, body aches, congestion.
π‘What should you do after reading everything above?
Well for certain, you shouldnβt panic because weβre not at the point yet where panic is warranted. The truth is, thereβs not enough data to show that this variant is a major concern yet - just simply something to keep an eye on - hence, itβs newly gained title VOC (Variant of Concern). As I mentioned earlier, there is a worry this variant could outcompete DELTA, which is concerning as it could then sweep across countries and continents just like Delta when it became the dominant strain 6+ months ago. But again, weβre not there yet.
Unfortunately the US public health officials are yet again failing us on this one. They are complacent and without conjecture regarding the implemented travel ban on South Africa. Such draconian measures are not based in science and do not slow the spread of any virus let alone SARS-CoV-2. Instead, said protocols hurt neighboring countries, place stigma , and destroy economies that depend on the free passage of tourists from here to there, or vice versa. We lack appropriate randomised control trials to support such lockdowns. Be that as it may, donβt feel that you should pause your travel plans, miss important family events, or avoid that concert you may have purchased tickets for.
Importantly, you do have control of some things in this situation. For example, hand hygiene, social distancing, mask wearing, avoiding crowded spaces, vaccination if you want. Anyways, this article will be updated as new data comes in. Please refer back as frequently as youβd like. If you want to see updates youβll have to re-open this email, then find this article again on my Substack page.
*If you feel this article was helpful, please share with a friend so they too can learn
RESEARCH:
https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html#anchor_1632154493691
https://www.nature.com/articles/d41586-021-03552-w
https://www.nature.com/articles/s41564-021-00908-w
https://www.news-medical.net/health/What-is-a-Polybasic-Cleavage-Site.aspx
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