Virus Fitness Comparisons

Whether it’s assessing the degree to which a virus has been attenuated, comparing the cytolytic properties of two different field isolates, or probing the function of a viral gene, fitness comparisons are integral to both vaccine development and basic virology research.  Although it can be defined differently within different contexts, “fitness” often refers to how efficiently a virus is able to pass through its entire life cycle – spanning everything from attachment, penetration, uncoating, replication, assembly, to virion release.  Because they can detect changes in the host cell throughout the continuum of a virus-induced CPE, and because they tracks these changes in real-time, xCELLigence-based assays are very well suited for virus fitness studies.

Viral hemorrhagic septicemia virus (VHSV) has a negative strand RNA genome that contains a highly conserved nucleotide sequence at its 3’ terminus which is predicted to form a hairpin structure (Figure A).  Øystein Evensen and colleagues at Norwegian University of Life Sciences sought to understand whether this sequence has an effect on VHSV replication and transcription in fish epithelial cells.  Working with a panel of VHSV mutants, total positive strand RNA levels were quantified using qPCR two days post-infection.

As seen in Figure B, whereas the U8C and A7C-U8A mutants had no discernable impact on viral positive strand RNA levels, the A4G-G5A mutant reduced viral RNA levels significantly.  xCELLigence was then used to assess the relative virulence of these different mutants (Figure C; virus was added to cells at the 72 hour time point).  Consistent with its reduced RNA levels, the A4G-G5A mutant (green curve) required a much longer time than WT virus (black curve) to effect complete killing of target cells.  Interestingly, the A7C-U8A mutant (blue curve) also showed a delayed onset of CPE even though its RNA levels were equivalent to WT.  Moreover, the U8C mutant (red curve) was actually more efficient than WT at killing target cells, despite having similar levels of RNA.  This example from VHSV highlights the fact that biomarker (such as RNA) quantifications do not always provide the whole truth of virulence and can be misleading when it comes to evaluating viral fitness, and demonstrates the utility of a functional assay that tracks the entire lifecycle of the virus.

The 3’ terminal sequence of the VHSV genome has an impact on both viral fitness and RNA levels. (A) Predicted secondary structure of the 3’ terminus of the VHSV genome.  (B) Total VHSV positive strand RNA levels two hours post infection.  (C) Quantifying the relative fitness of VHSV mutants using xCELLigence.  Data adapted from reference 1.

Another example of xCELLigence being used to quantitatively evaluate viral fitness involves bluetongue virus, which causes an economically important haemorrhagic disease in both wild and domestic ruminants (cows, sheep, and goats).  Bluetongue virus has a dsRNA genome that is arranged in 10 different linear segments.  By nature of this genome architecture, and the fact that multiple strains of the virus can infect a cell at the same time, bluetongue virus displays substantial genetic reassortment over time.  An important question is how this genome rearrangement affects viral virulence.  To address this,  Estelle Venter and colleagues at University of Pretoria generated variants of the virus where the bulk of the genome was derived from one strain, but included a fragment from a different strain.  The ability of these reassortant strains to kill Vero cells was then monitored in real-time by the xCELLigence system.  As seen in the below figure, parental strain 8 kills the target cells much more efficiently than does parental strain 6.  Interestingly, adding a fragment of the strain 8 genome to the strain 6 genome does not improve its cytopathogenicity: the killing kinetics of this chimera are actually slower.  In contrast, adding a fragment of strain 6 to the genome of strain 8 yields a virus with superior cell killing capabilities.

This ability to track these different viral phenotypes with precision enabled the authors to predict how bluetongue virus likely behaves in vivo.  Of special importance is the notion that a live attenuated strain of bluetongue virus being used to vaccinate animals could potentially rearrange with other strains in vivo, and thereby move beyond the attenuated phenotype to achieve viremias high enough to result in bona fide disease.


Reassortment of the bluetongue virus genome gives rise to differences in cytopathogenicity. Vero cells were grown to confluence and then infected (at 23 hours) with identical MOIs of either parental strains or genetic reassortant strains.  Data adapted from reference 2.

Vaccine handbook

Handbook: Explore Viral Cytopathic Effect Assays for Virology and Vaccine Research

  • Viral Titer Determination
  • Detection and Quantification of Neutralizing Antibodies
  • Studying Anti-viral Drugs
  • Testing Virucides
  • Oncolytic Viruses
  • Assessing virus quality/fitness

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Virus webinar

Webinar on Demand: A Groundbreaking Technology for Vaccine Development: New Techniques in Viral CPE Assessment using Real Time Cell Analysis

On Thursday, Nov 29, 2018 at 10am EST, Loic Benair (Sanofi Pasteur, France) and Brandon Lamarche (ACEA Biosciences) will describe new approach aimed at quantifying viral cytopathic effects during vaccine development.

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App note 18

Application Note 18: A New Way to Monitor Virus-Mediated Cytopathogenicity

A demonstration on the experimental workflow and the power of real-time impedance-based technology to evaluate viral cytopathic effects. 

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xCELLigence instruments that are compatible with virology/vaccine applications:

Dual PurposeSingle PlateMulti PlateHigh Throughput
3×16 wells1×96 wells6×96 wellsUp to 4×384 wells

  1. Specific nucleotides at the 3′-terminal promoter of viral hemorrhagic septicemia virus are important for virulence in vitro and in vivo.  Virology. 2015 Feb;476:226-32.
  2. Viral replication kinetics and in vitro cytopathogenicity of parental and reassortant strains of bluetongue virus serotype 1, 6 and 8.  Vet Microbiol. 2014 Jun 25;171(1-2):53-65.