Variant Alerts: Second Generation SARS-CoV-2 Variants Emerging And Gaining Prevalence, India-B.1.1/S:V1230L, Columbia-B.1.621, Mexico-B.1.1.519

Variant Alerts: More good news, as mankind arrogantly assumes that it has conquered the COVID-19 pandemic via its alleged successful vaccination programmes, more second generation SARS-CoV-2 variants are emerging and starting to becoming more predominant in circulation.


 
Thailand Medical News has already issued already warnings that a more catastrophic global surge ie expected sometime in late July or August and we are introducing more potential players to this surge and also some unique characteristics in the emerging second and third generation variants.
https://www.thailandmedical.news/news/beware-countries-like-israel,-britain-and-america-should-not-assume-that-the-worst-of-the-covid-19-pandemic-is-over,-the-worst-is-yet-to-come
 
https://www.thailandmedical.news/news/thailand-medical-news-apologizes-about-a-prediction-that-a-new-catastrophic-covid-surge-will-occur-in-august-new-study-shows-it-will-start-earlier-in-
 
https://www.thailandmedical.news/news/good-news-for-vaccine-manufacturers,-more-deadly-b-1-616-and-the-ap-n440k-variants-that-have-emerged-are-gaining-gradual-dominance-in-circulation
 
More emerging key players:
 
India Has A New Concerning Variant Emerging, The B.1.1/S:V1230L Variant
 
India is already facing a catastrophic surge but things are going to get far worse in India in a matter of weeks.
 
Indian researchers performed mutational analysis of the protein coding genes of SARS-CoV-2 strains (n=2000) collected during January 2021 to March 2021.
 
Alarmingly the study revealed the emergence of a new variant in West Bengal, India, which is characterized by the presence of 11 co-existing mutations including D614G, P681H and V1230L in S-glycoprotein. This new variant was identified in 70 out of 412 sequences submitted from West Bengal.
 
Importantly, among these 70 sequences, 16 sequences also harbored E484K in the S glycoprotein. Phylogenetic analysis revealed strains of this new variant emerged from GR clade (B.1.1) and formed a new cluster.
 
The study team proposed to name this variant as GRL or lineage B.1.1/S:V1230L due to the presence of V1230L in S glycoprotein along with GR clade specific mutations. Co-occurrence of P681H, previously observed in UK variant, and E484K, previously observed in South African variant and California variant, demonstrates the convergent evolution of SARS-CoV-2 mutation.
 
The V1230L mutation present within the transmembrane domain of S2 subunit of S glycoprotein, has not yet been reported from any country. Substitution of valine with more hydrophobic amino acid leucine at position 1230 of the transmembrane domain, having role in S protein binding to the viral envelope, could strengthen the interaction of S protein with the viral envelope and also increase the deposition of S protein to the viral envelope, and thus positively regulate virus infection.
 
The P618H and E484K mutation have already been demonstrated in favor of increased infectivity and immune invasion respectively.
 
Hence alarmingly  the new variant having G614G, P618H, P1230L and E484K is expected to have better infectivity, transmissibility and immune invasion characteristics, which may pose additional threat along with B.1.617 in the ongoing COVID-19 pandemic in India.
 
The study findings were published on a preprint server and are currently being peer reviewed. https://www.medrxiv.org/content/10.1101/2021.05.24.21257705v1
 
New Variant Debuts In Already Ravaged Columbia, The B.1621 Variant.

SARS-CoV-2 genetic diversity has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited neutralizing antibodies.
 
Columbian researchers report the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several mutations affecting the Spike protein, including the amino acid changes I95I, Y144T, Y145S and the insertion 146N in the N-terminal domain, R346K, E484K and N501Y in the Receptor Binding Domain and P681H in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in some cities that were near the theoretical herd immunity suggests an epidemiologic impact. Studies are underway to assess the biological and epidemiologic roles of the substitution pattern found in the B.1.621 lineage.
https://www.medrxiv.org/content/10.1101/2021.05.08.21256619v1
 
Mexico Reports Emergence Of Variant That Has Potential To Evade Vaccine Effects.
 
SARS-CoV-2 variants have emerged in late 2020 and there are at least four variants of concern (B.1.1.7, B.1.351, P1, B.1.617) reported by WHO. These variants have several substitutions in the Spike protein that affect receptor binding; they present increased transmissibility and may be associated with reduced vaccine effectiveness.
 
Researchers in Mexico have reported the identification of a potential variant of interest harboring the mutations T478K, P681H, and T732A in the Spike protein, within the newly named lineage B.1.1.519, which rapidly outcompeted the preexisting variants in Mexico and has been the dominant virus in the country during the first trimester of 2021. This new variant is expected to be upgraded to the status of a Variant of Concern(VOC) in coming weeks. https://www.medrxiv.org/content/10.1101/2021.05.18.21255620v1
 
More Breakthrough Infections Among The Vaccinated
 
Already it has been seen that there is an ever growing number of breakthrough infections in individuals that have been vaccinated with the current COVID-19 vaccines and these numbers are growing each day as reported by the U.S.CDC. https://www.newsweek.com/cdc-breakthrough-infections-1594696
 
Interestingly most of these breakthrough infections are being caused by Variants of Concern which many vaccine manufacturers claim they are able to eradicate with their current vaccines. https://www.medrxiv.org/content/10.1101/2021.05.23.21257679v1
 
It is also interesting to note that the same U.S CDC has also recently changed the standards of the PCR testing to sort of ‘enhance’ the vaccination efforts! https://www.minareport.com/2021/05/23/us-based-cdc-changes-pcr-tests-to-make-vaccines-look-successful/
 
Not Enough Attention Is Being Paid To Mutations or Molecular Changes On The Nucleocapsid Proteins Of The Second And Third Generation Variants.
 
An interesting phenomenon among most of the newly emerging second and third generation variants of the SARS-CoV-2 coronavirus is the appearance of more mutations and even molecular changes such as dimerization on the nucleocapsid proteins. Unfortunately most researchers and vaccine manufacturers are too engrossed on the spike proteins.
 
Some of the new molecular changes such as dimerization of the nucleocapsid proteins found in the new variants allow them to go undetected with the current PCR tests. This is concerning as there are many new variants out there that are not being detected!
https://www.biorxiv.org/content/10.1101/2021.05.23.445305v1
 
Also it has been found that mutations on the nucleocapsid proteins of emerging variants are increasing the infectivity and fitness potential of these new variants. https://www.biorxiv.org/content/10.1101/2021.05.24.445386v1
 
Contrary to popular beliefs, the SARS-CoV-2 coronavirus is evolving much faster and more variants are emerging faster driven by the current vaccination programmes and antibody orientated protocols. https://www.biorxiv.org/content/10.1101/2021.05.23.445341v1
 
As Thailand Medical News has always been warning, there is an urgent need to spend efforts on developing effective antivirals, preferably a combo approach of antivirals as coronaviruses are known to evolve fast and develop drug resistance.
 
On a more important aspect, there is a need to focus on research regarding harvesting the therapeutic potential existing in the great natural diversity of plants and herbs and the many potent phytochemicals in them. More efforts and government incentives are needed in this area instead of expensive toxic pharmaceuticals.
 
For the latest Variant Alerts, keep on logging to Thailand Medical News.