Next Lethal SA 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, 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.
Analyses were performed 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, it was found that there are 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. Using 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. It was found that multiple mutations have occurred in the samples.
The 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 effi cacy.
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