BREAKING! While The World Has Been Occupied With Omicron, Two New Delta Sublineages Threats - AY.43.1 And AY.43.2 Are Busy Gaining Ground
While the world has been over preoccupied with the Omicron variant, two new sub-lineages from a Delta Subvariant AY.43
have emerged in Brazil with worrying mutations that that indicate possible enhanced transmissibility and immune evasiveness coupled with drastic changes in viral functions.
The two new novel Brazilian sub-lineages AY.43.1 and AY.43.2 belonging to the Delta AY.43 subvariant lineage. Both the novel sublineages were defined by the following characteristic nonsynonymous mutations: ORF1ab:A4133V and ORF3a:T14I for AY.43.1 and ORF1ab:G1155C for AY.43.2.
According to local physicians and medical experts, the two new variants could be behind the new small cluster surges in Brazil originating in Sao Paulo with many who were fully vaccinated before or had previous infections getting re-infected and displaying moderate to severe symptoms.
Local health authorities are saying that it is still too early to make any inferences and more studies are needed to assess the situation.
A team of researchers from Sao Paulo University and the Butantan Institute in Brazil have already published a preprint paper on the discovery of this new Delta sub-lineages. https://www.medrxiv.org/content/10.1101/2021.11.29.21266819v1
The SARS-CoV-2 delta variant is so diverse with more than 120 sublineages within the Pango lineages and another 28 that is still being classified and not uploaded yet.
Despite more than 157 million doses of the anti-SARS-CoV-2 vaccine administered and approximately 124 million people fully vaccinated and the fact that Brazil is one of the most vaccinated nations globally, sporadic cluster and rising COVID-19 infection rates in certain areas are posing a new threat .
Some experts believe that this high vaccination rate may also help in the selection of novel SARS-CoV-2 lineages and sublineages because of the accumulation of viral mutations that lead to viral fitness.
Despite the preexisting gamma variant of concern (VOC) being fully replaced by the delta VOC in Brazil, new Delta sub-lineages like these could pose a new threat not only to Brazil but also the rest of the world.
The study team characterized the two novel AY.43 sublineages of the SARS-CoV-2 delta variant with probable Brazilian origin. This was attributed to the observed specific clustering and specific mutation profile in the phylogenetic tree generated by Nextstrain. The raw sequence data were submitted to quality control analysis using the FastaQC software and trimmed using Trimmomatic to select the best quality sequences. The trimmed sequences were mapped against the SARS-CoV-2 reference using BWA software and samtools for reading indexing. Pilon was used to refine the mapped files and obtain the correct indels and insertions and bcftools were used for variant calling and seqtk to assemble the consensus SARS-CoV-2 genomes.
The phylogeny of the AY.43 hypothetical sublineages was reconstructed using 1,616 SARS-CoV-2 sequences generated from the Butantan Network for Pandemic Alert of SARS-CoV-2 variants.
The study team identified AY.43.1 and AY.43.2 as the two novel Brazilian sublineages belonging to the AY.43 lineage.
Both the novel sublineages were defined by the following characteristic nonsynonymous mutations -ORF1ab:A4133V and ORF3a:T14I for AY.43.1 and ORF1ab:G1155C for AY.43.2. The majority of the analyzed sequences of both lineages originated from the city of São Paulo.
The study findings showed the crucial importance of the SARS-CoV-2 genomic surveillance to identify emerging lineages.
Alarmingly these emerging SARS-CoV-2 lineages may significantly impact the public health systems due to increased infectivity and transmission.
Importantly, the T14I mutation in the ORF3a shows deleterious effects on the viral proteins. A nonsynonymous mutation in a conserved protein ORF3a, involved in viral replication and release, may affect viral functions in addition to the mutational constellation defined for the SARS-CoV-2 Delta variant.
More detailed studies may explore the reason for disseminating the two sublineages in São Paulo State and Brazil and their potential impact on the ongoing vaccination process.
Many new Delta sub-variants and emerging sub-lineages are also being observed in many countries including in India, Myanmar, Philippines And Indonesia but there are very little efforts to monitor and study them. In it is only a matter of time that either these new Delta subvariants cause a major shift in the pandemic or they might recombine with other emerging or existing variants or even with new zoonotic variants and come up with something more catastrophic.
It should be noted that the molecular surveillance of the SARS-CoV-2 variants plays an important role in the rapid characterization of the virus and the accumulation of mutations that can alter the viral functions in terms of infectivity and transmissibility and help in implementing strategies to prevent their dissemination.
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Thailand Medical News will provide more updates on these new Delta Sub-lineage