The Next Lethal Variant Might Emerge From South-East Asia As WHO And The West Are Paying Little Vigilance In This Region. Indonesian Study Hints Possibility!
There is an extremely high possibility that the next lethal SARS-CoV-2 variant might actually emerge from South East Asia, from one of the countries like Indonesia, Philippines, Thailand, Myanmar or Cambodia. With vaccination rates that are still considered low plus a mix and match of various vaccines including the inferior quality Chinese vaccines and other adenovirus vector based vaccines being used coupled with low genomic sequencing and monitoring, a complacent population, corrupted and ignorant health officials and a high rate of other viral and bacterial infections spanning from HIV, Herpes, HPV, TB, Dengue, Malaria etc among the local population, it is little wonder that a possible lethal SARS-CoV-2 variant might emerge.
To make matters worse, in the outskirts of some of these countries, people are still trading and eating all kinds of wild animals and their proximity to certain wild life is also worrying. It should also be noted these countries also harbor large bat populations besides many other types of wild life (That are reservoirs for a variety of coronviruses) that some of the locals still relish as foods! Also, in most of these countries, there are more than one variant in circulation besides the Omicron. Unknown to any, some of these countries have already had the SAR-CoV-2 spawn its own local variants. For example, Indonesia has two local variants are more predominant than the known VOCs ie B.1.470 and B.1.466.2.
As the SARS-CoV-2 goes thru humans and communities, it also acquired mutations and in some cases these mutations can cause the emergence of a more transmissible, more immune evasive and more virulent and lethal SARS-CoV-2 Variant.
Alarmingly, a new Indonesian study has shown that besides the VOCs in circulation, even its own local variants are evolving and spotting newer mutations and in some cases these new mutations are enhancing the capabilities of the variants.
Researchers from the Swiss-German University at Tangerang, Indonesia in a new study involving whole-genome sequencing of the various variants isolated in Indonesia alarmingly found that multiple mutations have occurred in genes of these variants and it caused alterations in the characteristics of the virus and in some cases with the possibility to affect vaccine efficacy and also disease severity.
The study team conducted detailed analyses to investigate SARS-CoV-2 prevalence in Indonesia using data obtained from GISAID.org. A whole-genome sequencing was performed on the random samples taken from GISAID.org utilizing the BLAST tool from NCBI. The variants identified in Indonesia are Alpha, Beta and Delta variants, as well as local variants B.1.470 and B.1.466.2.
As of the end of November 2021, it was found that there were a total of 5,348 cases of the Delta, 78 cases of the Alpha, 22 cases of the Beta, 572 cases of the local variant B.1.470, and 1.833 cases of the local variant B.1.466.2. Other cases include 219 cases of local variant B.1.1.398, 160 cases of local variant B.1.459 and 1.028 cases of the wild type.
In total there are 9,260 isolated genomes collected in
GISAID that are located in Indonesia.
Utilizing BLAST, WGS of Alpha, Delta, Beta, B.1.470 and B.1.466.2 variants isolated in Indonesia was compared with the wild type from Wuhan NC.045512.2.
The study findings found that multiple mutations have occurred in the samples.
The new mutations identified as are H69del, V70I, N501Y, D614G, A570D, P681H, T716I, S982A, and D1118H in the Alpha variant, T19R, L452R, T478K, D614G, and D950N in the Delta variant, D215G, D614G, A701V, L241-, L242-, K417N in the Beta variant, D614G, L242F, and S12F in the B.1.470 variant and D614G, N439K, and P681R in the B.1.466.2 variant. These mutations had caused alterations in the characteristics of the virus and how it may affect vaccine efficacy.
In the Alpha variant, four mutations need to be considered because they affect the characteristics of the virus, causing an increase in cleavage of the S1/S2 and in turn increasing the infection rate. However, the Alpha variant does not drastically reduce the efficacy of the vaccines.
Moreover, the Delta variant mutations can reduce immunity and increase replication, making it easier to spread which could explain why it is the most common variant in Indonesia. Despite this, the efficacy and effectiveness of the vaccine is only slightly reduced by Delta. As for the Beta variant, it was observed that the virus's mutations can bind to the neutralizing antibody, affecting the work of the antibodies and thus reducing the efficacy of the vaccines at a higher level than the other variants.
In the case of the local variants B.1.470 and B.1.466.2, they were seen to have several shared mutations with other the variants (Alpha, Beta, and Delta variants), with these mutations increasing the infection rate as well as enhancing the replication of the virus.
However alarmingly, of these local variants, the B.1466.2 variant gained one new mutation that may cause more infections, and that mutation is N439K. This mutation can bind to the hACE2 with higher affinity than the wild-type and can also neutralize antibodies of the vaccines.
The study findings were published on a preprint server: Research Square and are currently being peer reviewed. https://www.researchsquare.com/article/rs-1225245/v1
The study findings from whole-genome sequencing of variants isolated in Indonesia have found that multiple mutations have occurred in genes of the SARS-CoV-2 variants which are causing alterations in the characteristics of these variants and may affect vaccine efficacy. It should be noted that classification from the GISAID website may change overtime. The result in this paper is based on the data taken at the end of November.
It is important that the WHO, The US.CDC, The ECDC and genomic researchers pay careful attention to what is brewing in these South East Asian countries as even these local Indonesian variants such as the B.1.470 and B.1.466.2
variants are not listed or found in many of the variant listings maintained online by many the Western genomic specialists and open access platforms besides GISAID.
It will even be more surprising for the Western experts to find out what has been really happening in the rest of the mentioned countries besides Indonesia as we have access to non-verified data that in one of these countries, at least two local variants have also emerged but the local authorities are clamping down on any mention about it as they fear it will adversely affect their economy and tourism industry!
For more on the next lethal SARS-CoV-2 Variant
, keep on logging to Thailand Medical News.