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Updated: Sep 21, 2025

Author Spotlight: A Pseudotype Virus System for Assessing Omicron Subvariants and Neutralizing Antibodies in SARS-CoV-2 Research

Author Spotlight: A Pseudotype Virus System for Assessing Omicron Subvariants and Neutralizing Antibodies in SARS-CoV-2 Research

Published on: September 8, 2023

Convolutional Neural Networks Based on Sequential Spike Predict the High Human Adaptation of SARS-CoV-2 Omicron

Bei-Guang Nan¹, Sen Zhang¹, Yu-Chang Li¹

¹State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Milltary Medical Sciences, Beijing 100071, China.

|May 28, 2022

Summary

A new deep learning model accurately predicts SARS-CoV-2 variant transmissibility. The model identified Omicron BA.2 as more adaptive and faster spreading than BA.1/BA.1.1 sublineages.

Keywords:

Omicron SARS-CoV-2 adaptation deep learning sequential amino acid frequency

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Published on: June 5, 2021

Area of Science:

Virology
Genomics
Computational Biology

Background:

The COVID-19 pandemic has seen the emergence of highly transmissible SARS-CoV-2 variants, like Omicron and its sublineages.
Distinguishing high-risk SARS-CoV-2 variants, particularly Omicron sublineages, remains a significant challenge.

Purpose of the Study:

To develop a fine-grained deep learning (DL) model for assessing SARS-CoV-2 transmissibility.
To update a previous coarse-grained model using sequential Spike protein data.

Main Methods:

Sequential amino acid (AA) frequency in the Spike protein was decomposed into windowed fragments.
Unsupervised machine learning identified distributions in AA frequency.
A supervised Convolutional Neural Network (CNN) was trained with three adaptation labels to predict human adaptation in Omicron sublineages.

Main Results:

Clear separation between SARS-CoV-2 lineages and clustering within lineages were observed in decomposed sequential AAs.
The DL model accurately classified variants based on differing adaptations.
Omicron BA.2 was predicted to have higher human adaptation than BA.1/BA.1.1 sublineages.

Conclusions:

The Omicron BA.2 sublineage exhibits greater adaptability and has spread more rapidly, especially in Europe.
The fine-grained DL model effectively assesses SARS-CoV-2 variant transmissibility in a timely manner.
This model aids in controlling the spread of emerging SARS-CoV-2 variants.