Accelerating the Development of a Rapid Detection NAAT Assay for SARS-CoV2

Overview

Rapid and accurate molecular diagnostics are essential for detecting viral pathogens such as SARS-CoV-2. Nucleic Acid Amplification Tests (NAAT) rely on highly specific primers and probes to ensure precise detection while avoiding cross-reactivity with other pathogens. Achieving this level of specificity requires comprehensive analysis of viral sequence variants and genomic alignments.

A pharmaceutical company partnered with Excelra to accelerate the development of a rapid detection NAAT assay for SARS-CoV-2. By applying expertise in Bioinformatics Solutions, Computational Biology, and Scientific Informatics, Excelra delivered an integrated workflow that enabled in-silico analysis of primer and probe sensitivity and specificity while identifying critical variant prevalence patterns.

Our client

The client is a pharmaceutical company based in the European Union working in the field of molecular diagnostics for infectious diseases. Their research focused on improving SARS-CoV-2 detection assays by ensuring the accuracy and reliability of probe and primer sequences used in NAAT-based diagnostic platforms

Client’s challenge

The client aimed to perform in-silico sensitivity and specificity analysis of probes and primers for SARS-CoV-2 molecular diagnostic assays.

Key challenges included:

• Extracting variant prevalence data from large sequence alignment datasets
• Ensuring primer/probe sequences specifically target SARS-CoV-2 without cross-reactivity
• Analyzing gene variants from filtered, non-redundant sequence alignments
• Obtaining structured outputs of variant prevalence for genes of interest
• Accelerating assay development while maintaining diagnostic accuracy

These challenges required specialized expertise in genomic analysis and data processing workflows to reduce development timelines and ensure robust assay design

Client’s goals

The client sought to:

• Retrieve and analyze SARS-CoV-2 genomic sequence alignments
• Identify gene variants relevant to diagnostic assay development
• Analyze variant prevalence across geographic regions and time
• Validate probe and primer specificity against non-target pathogens
• Generate structured outputs for gene variant analysis

Achieving these objectives would help the client accelerate the development of reliable molecular diagnostic assays.

Our approach

Excelra implemented a structured computational workflow to analyze SARS-CoV-2 genomic data and support rapid NAAT assay development.

Sequence data acquisition

Excelra retrieved SARS-CoV-2 multiple sequence alignments from trusted genomic databases such as Nextstrain and GenBank. These datasets provided comprehensive viral sequence information for downstream variant analysis

Variant prevalence analysis

The team conducted in-depth analysis of gene variants for the two genes of interest, evaluating variant prevalence across:

• Geographic regions
• Time periods
• Viral sequence datasets

A custom script was developed to extract variant information and perform prevalence analysis at scale.

Specificity testing for primer and probe sequences

To ensure diagnostic accuracy, Excelra evaluated primer and probe sequences against genomes of common human pathogens.

This step ensured that the assay would accurately detect SARS-CoV-2 while avoiding cross-reactivity that could produce false positives.

Workflow development

Excelra designed a tailored computational workflow that enabled:

• Extraction of specific gene sequences
• Variant identification and filtering
• Prevalence analysis across datasets
• Automated data processing for molecular diagnostic research

The workflow significantly improved the efficiency of genomic data analysis.

Our solution

Excelra delivered a comprehensive in-silico analysis pipeline that enabled rapid development of the client’s NAAT assay.

Key outcomes

• Retrieval and processing of SARS-CoV-2 multiple sequence alignments
• Development of scripts for variant extraction and prevalence analysis
• Validation of primer/probe specificity against non-target pathogens
• Structured dataset of gene variants and prevalence information
• Identification and prioritization of variants relevant to assay development

These insights enabled the client to select optimal probe and primer sequences for their rapid detection assay.

Key benefits

• Improved assay accuracy
  In-silico specificity analysis ensured primers and probes targeted SARS-CoV-2 accurately without cross-reactivity.
• Accelerated assay development
  Automated workflows reduced the time required to analyze large genomic datasets.
• Actionable variant insights
  Variant prevalence analysis provided deeper understanding of viral mutations impacting diagnostic assays.