Development of a New Platform to Track SARS-CoV-2 Variants

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SARS-CoV-2

With the occurrence of the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2), entire world is trying its best to restore population’s health and well-being. Omicron variant is one of the five variants that is affecting many parts globally now.

According to Centre of diseases control, the following classes of SARS-CoV-2 variants have been established:

Variant Being Monitored (VBM)

  • Alpha (B.1.1.7 and Q lineages)
  • Beta (B.1.351 and descendent lineages)
  • Gamma (P.1 and descendent lineages)
  • 1.617.3
  • Mu (B.1.621, B.1.621.1)
  • Epsilon (B.1.427 and B.1.429)
  • Eta (B.1.525)
  • Iota (B.1.526)
  • Kappa (B.1.617.1)
  • Zeta (P.2) 

Variant of Concern (VOC)

  • Omicron (B.1.1.529 and BA lineages)
  • Delta (B.1.617.2 and AY lineages) 

COVID-19 Variants and Outcomes

All different variants of COVID-19 have undergone mutations, making them more virulent. Thus, it becomes critical to monitor the severity of these variants and track if there is any potential new SARS-CoV-2 variant.

Scientists under the guidance of Laura D. Hughes have created an online portal, Outbreak.info to monitor the wide spectrum of COVID-19 mutations and lineages. Presently, this portal is assessing 7000 locations with the aim to alert the public officials in case of any future public threat. This is providing real-time genomic surveillance. It is a scalable and dynamic tracking portal.

Developing the platform

Researchers measured the growth rate of the virus depending on its transmission and extent of spread. Mutations that increased the infection probability were determined. For example, Alpha variant had a higher spread (40% to 60%) compared to previous lineages. This allowed a faster spread and resulted in a dominant variant.

With the help of outbreak.info, genomic information can be categorized into three aspects including time, geography, and mutations. Initially, a lineage was defined based on the characteristic mutations. Hence, the rising numbers of SARS-CoV-2 genomes could be easily updated.

Genomic surveillance includes datasets and epidemiological data from sources such as John Hopkins University, LitCOVID, bioRxiv, and medRxiv.

Method for Genomic surveillance

The mutation or lineage tracker determines the growth rate of a lineage, mutation, or a combination of both.

The tracker examines the spread of the variant at a particular location and how its spread increases over time. For example, the Delta variant and its lineages spread rapidly. The Location Tracker determines the growth at different locations and levels such as city, state, and country. The growth rates are influenced by factors that affect population’s immunity including:

  • Availability of vaccines
  • Social mobility
  • Virus attack rate

Present classification and mutation of SARS-CoV-2

Based on the continuous evolution of the virus, variants have been categorized into these major categories.

  • Variant of Concern (VOC)
    Presently, variants that are considered to be infectious, so are being monitored closely by federal agencies.

Application of the platform to monitor the variants lineages

Delta variant has been diversified into numerous lineages, approximately 200 lineages. Studies have shown that depending on the location the spread of these variants vary. For example, the most prevalent variant in U.S and U.K were B.1.617.2 and B.1.617.2 respectively.

On the other hand, Omicron has higher transmission rate compared to Delta variants. For example, the dominant lineage of Omicron is BA.1 while in countries such as India, Denmark and Singapore, BA.2 has been identified.

Conclusion

Timely identification of various variants will impede the spread of virus. This will allow to track the transmission and prevent other regions of its deleterious effects.

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