Recently bioRxiv * preprint study, researchers from the University of Hawaii showed that the S gene of the acute acute coronavirus 2 (SARS-CoV-2) respiratory syndrome is increasingly moving according to the sequence and phylogenetic analysis. At the same time, a specific snoring with a mutation emerging in a modified spike glycoprotein may be present in Hawaii.
Over the past year, there has been a significant evolution of SARS-CoV-2 worldwide, which remains a major threat. As of January 2021, four novel viral changes have been reported from the United Kingdom (VOC 202012/01 / B.1.1.7), South Africa (501Y.V2), Nigeria (B.1.207), and Denmark (Mink Cluster V ).
Such a rapid and stable rate of evolutionary changes affects the pathogenity of SARS-CoV-2, a causative agent of coronavirus infection (COVID-19), and certainly deserves further studies. In other words, an in-depth look at the genome is needed to evaluate all genomic changes and mutations.
It is already known that mutations in the viral spike glycoprotein can alter binding efficiency and, therefore, viral fitness. In fact, some nucleotide sequences in the SARS-CoV-2 gene can alter the pathogenity and muscle reduction, which is why they have become dangerous in monitoring the release of virus.
In this study, the researchers from the University of Hawaii (led by David P. Maison, MS) report an analysis of the SARS-CoV-2 S 969-bp gene from two Hawaiian patients to determine the value of bring about changes in the glycoprotein spike, which is also a key target used by vaccines.
Generating phylogenetic trees
At the John A. Burns School of Medicine Biocontainment Facility at the University of Hawaii, ribonucleic acid (RNA) was extracted from a nasal swab and oropharyngeal swab from two male patients (average age 29.5 years) with the SARS-CoV- 2 in the August 2020.
Following a polymerase chain reaction (PCR), the two viral sequences were followed using a Sanger sequence (also known as the “chain termination method”). The latter was applied to the amplicons using four primers (CF, CR, CR2, and CR3).
In addition, phylogenetic trees were created using MEGAX (ie, an integrated tool for automatic and manual series alignment). The alignment was first performed using the MUSCLE program, and then created with Load Appearance parameters with 1,000 bootstraps.
SARS-CoV-2 S Gene Region is used in this Study Together with Anotated Primers, Mutations, and Cysteine Residues of the Receptor Binding Land Figure representing Hawaii strain strains MW237663 and MW237664. The primer pair, CF / CR, was used to increase the 1,127-bp S gene fragmentation and CF, CR, CR2 and CR3 primers shown with purple boxes were used for the Sanger series. The yellow box marks the beginning and end of the 969-bp series. The blue line marks the 3 ‘end of the S gene receptor binding domain (RBD). Remains of cysteine RBD are shown in picture boxes. All mutations found in this study are in their own loci with nucleotide numbers and rectangular boxes connecting to the sensory strand as indicated after the nucleotide number and subset. in the figure (nucleotide / protein mutations: G23126T / A522S, C23185T / F541F, T23189C / F543L, C23291T / R577C, A23312G / I584V, A23403G / D614G, C23601G / S680C, C2360 / A E780Q, C23929G / T790 All boxes are gray except for the P681H mutation shown in Hawaii series from this study, shown with a yellow rectangle.Image was created by the SnapGene software (from Insightful Science; available at snapgene.com) and created by BioRender.com.
Emerging features of P681H mutation
In short, Hawaiian SARS-CoV-2 series deposited in the GenBank in March 2020 were compiled by series from Wuhan, China, Sweden, and the state of New York (USA). The SARS-CoV-2 rays in this study were collected from Washington state (USA), as well as strains from China and Hawaii.
In addition, phylogenetic tree findings suggest that the virus was introduced to Hawaii from multiple sources. Thirteen single nucleotide polymorphisms were decoded across 13 specific SARS-CoV-2 genomes within the S gene segment – with one nonspecific mutation (P681H) detected in the two Hawaiian sequences.
This prestigious P681H press has special features that feature it, with an abstract increase in global frequency compared to the D614G (currently universal) simulation platform. Similarly, P681H mutation is also a typical feature of the new SARS-CoV-2 variants found in the United Kingdom and Nigeria.
A number of mutations that caused cysteine residues were also detected, with possible consequences such as disruption of the disulfide bridges in and around the receptor binding domain of the viral spike glycoprotein.
Potential viral clearance
This study in fact shows a series of sequences from the first SARS-CoV-2 sequence that harbor the insensitive P681H imitation. Therefore, further studies are needed to investigate the pathogenity and violence of this mutation in Hawaii strains and whether it can be considered as a viral clearance method to delay antibody recognition.
“In Hawaii, Indigenous Hawaiian and Pacific Islanders have a high incidence of SARS-CoV-2 compared to other ethnic minorities and Whites”, say study authors here bioRxiv paper. “Identifying viral strains from these minority groups is important for a better understanding of virus transmission and pathogenity”, they add.
Going forward, targeted order identification will be required to circulate a multiple-input source of SARS-CoV-2 in Hawaii, which will subsequently inform similar studies in other parts of the world. world.
* Important message
bioRxiv publish preliminary scientific reports that are not peer-reviewed and, therefore, should not be seen as final, guiding health-related clinical practice / behavior, or be treated as information established.