Whole-Genome Sequence Analysis of DELTA Variant at Ayass BioScience, LLC

The Delta variant was first detected in India in October 2020. By June 1, it had spread to 62 countries. Two weeks later, it had been found in 80 countries and by July 4, the number had risen to 104.

The delta variant is the most contagious version of the coronavirus. It spreads 225% faster than the original version of the virus, and it’s currently dominating the outbreak not only in the United States, but worldwide.

Recently Published Study shows why. The variant grows more rapidly inside individual’s respiratory tracts and to much higher levels. People infected with the delta variant have 1,000 times more copies of the virus in their respiratory tracts than those infected with the original strain of COVID-19.

Recently, the Delta variant of SARS-CoV-2, a viral lineage also known as B.1.617.2 that was first identified in India, has been considered the “greatest threat” in the world’s effort to contain COVID-19. To assess the incidence of the Delta variant from a local laboratory and investigate any vaccine breakthrough cases against the Delta variant, our lab performed the viral whole-genome sequence analysis on 35 samples randomly select from nasal swab positive cases that were tested from June 1st to July 30th, 2021. Number of cases surveyed is 27.

44% of surveyed SARS-CoV-2 positive cases were not vaccinated. Of those who received vaccines, 44% were vaccinated with Pfizer-BioNTech, 4% with Moderna, and 7% with Johnson & Johnson’s Janssen. 25 cases out of surveyed COVID-19 positive cases were identified as Delta Variants.

The laboratory continues to sequence the positive samples and starts to see a rise in the number of cases of Delta variant of COVID-19 that have been previously vaccinated. The initial data suggests that the Delta variant is spreading quickly in our communities and the public may have a potential risk to infect COVID-19 even full vaccinated.

The cases also supported the idea that continued travel-related control measures and public health mitigation measures such as:

Wearing masks
Physical distancing
Daily symptom screening
Regular testing
Avoiding crowds
Avoiding unnecessary travel
Obtaining a full vaccination

It is critically important for public health to slow down the spread of the SARS-CoV-2 virus and accelerating the end of the pandemic.

Ayass BioScience’s Delta Variant Sequencing Cases Summary

Why we need to sequence SARS-CoV-2 viral variants:

  1. Investigating virus transmission dynamics and introductions of novel genetic variants;
  2. Investigating the relationship between clades/lineages and epidemiological data such as transmissibility and disease severity or risk groups to guide public health action;
  3. Understanding the impact of response measures on the virus population;
  4. Assessing the impact of mutations on the performance of molecular diagnostic, serological, and antigen detection methods;
  5. Assessing relatedness of viral strains within epidemiological clusters and supporting contact tracing and other public health interventions;
  6. Assessing and confirming reinfections;
  7. Prompting further basic research investigation to confirm relevance of observed mutations in the pathogenesis of the disease (e.g. infectivity, receptors binding);
  8. Assessing the impact of mutations on the performance of antiviral drugs;
  9. Assessing the impact of mutations and modelling the antigenic properties of the virus to assess the risk of vaccine escape;
  10. Assessing the potential incidence of vaccine-derived virus infections and transmissions should live SARSCoV-2 vaccines become available.

https://www.cdc.gov/coronavirus/2019-ncov/variants/variant.html

Date of designation – VOI – 4 April 2021, VOC – 11 May 2021. In October 2020 B.1.617 emerged in India, causing an rapid increase in COVID-19 cases across the country. The lineage is further divided into three subgroups: B.1.617.1, B.1.617.2, and B.1.617.3; of which the B.1.617.2 variant has been designated as Variant of Concern (VOC) because of significantly increased infectivity.

B.1.617.2 variant contains nine spike mutations, including five mutations in the N-terminal domain (NTD), 2 mutations in the receptor-binding domain (RBD), 1 mutation in the furin-cleavage site, and one mutation in the spike S2 subunit.

GeneNucleotideAmino acid
ORF1abC14408TP4715L
G15451AG5063S
C16466TP5401L
SpikeC21618GT19R
22029-22034 delAGTTCA
EF 156-157 deletion
G21987AG142D
T22917GL452R
C22995AT478K
A23403GD614G
C23604GP681R
G24410AD950N
ORF3AC25469TS26L
MT26767CI82T
ORF7AT27638CV82A
C27752TT120I
ORF828248-282530 delGATTTCDF 119-120 deletion
NA28461GD63G
G28881TR203M
G29402TD377Y

Transmissability: Increased
Virulence: Likely Increased
Antigenicity: B.1.617.2 variant is resistant to therapeutic monoclonal antibodies, natural infection’s or vaccine-induced antibodies.
Spread: Originally was discovered in India and has now spread to more than 100 countries. Variant is dominant in India & UK now (and many other Asian countries where sequence data is not widely available), but prevalence also growing fast in US, as well as many European countries.

Global Positive Samples Sequenced: 2,167,558

B.1.617.2 Sequenced: 163,338

% of Global Samples Sequenced: 7.54%

Distribution of B.1.617.2 Sequences Top 5 Countries: United Kingdom 76.0%, India 8.0%, United States of America 5.0%, Germany 2.0%, Singapore 1.0%

(Predominantly India lineage with several spike mutations.)

Updated July 2021

Ayass BioScience, LLC are sequencing positive COVID-19 cases to find new mutations:

Evidence strongly suggests that the Delta variant poses the most significant risk to unvaccinated populations. If you are worried about DELTA or other variants, get vaccinated now at our location: