VIPERA

VIPERA integrates the evaluation of intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection.

Key Features:

• Ancestry Evaluation: VIPERA evaluates the intra-patient ancestry of SARS-CoV-2 sequences from serial samples.
• Trajectory Analysis: VIPERA analyzes evolutionary trajectories of serial sequences from the same viral infection.
• Population Dynamics Detection: VIPERA reveals population dynamics within intra-patient viral populations.
• Adaptive Evolution Detection: VIPERA identifies evidence of adaptive evolution in chronic SARS-CoV-2 infections.

Scientific Applications:

• Chronic Infection Analysis: VIPERA analyzes SARS-CoV-2 viral evolution within patients during chronic infections.
• Variant of Concern Surveillance: VIPERA studies intra-patient mutations that may nurture the adaptive potential of SARS-CoV-2 as a potential source of variants of concern.
• Serial Sample Comparison: VIPERA compares serial sequences from the same viral infection to track evolutionary changes over time.

Methodology:

VIPERA was validated using positive and negative control datasets before application to clinical cases.