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{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Virus particle abundance |- | '''Approach:''' epifluorescence microscopy, flow cytometry, plaque assay, or MPN |- | '''Context:''' ''in situ'', incubation, lab |- | '''Spatial scale:''' point sampl..."

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Created page with "{{BreadcrumbsInteractions}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Virus particle abundance |- | '''Approach:''' epifluorescence microscopy, flow cytometry, plaque assay, or MPN |- | '''Context:''' ''in situ'', incubation, lab |- | '''Spatial scale:''' point sampl..."

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* [[Page authors|Page authors]]: [[PRIMO]]
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<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! Virus particle abundance
|-
| '''Approach:''' epifluorescence microscopy, flow cytometry, plaque assay, or MPN
|-
| '''Context:''' ''in situ'', incubation, lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' hours to days (changes in abundance)
|-
| '''Units:''' particles L<sup>-1</sup>; particles cell<sup>-1</sup> (burst size)
|-
| '''Community captured:''' bulk viral community
|-
| '''Co-measurements:''' host cell abundance
|}
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<div style="clear:both"></div>

== Method Overview ==

Virus-like particle (VLP) concentrations in seawater are determined by one of several approaches: (1) Epifluorescence microscopy after staining with SYBR Green I or DAPI: filtered samples on anodisc or polycarbonate membranes are stained with a nucleic-acid-specific fluorescent dye and counted under the microscope. (2) Flow cytometry: samples are stained with SYBR Green I and run on a flow cytometer; VLPs are resolved as a distinct population based on their green fluorescence and side scatter<ref name="Marie1999">Marie, D., Brussaard, C. P. D., Thyrhaug, R., Bratbak, G., & Vaulot, D. (1999). Enumeration of marine viruses in culture and natural samples by flow cytometry. ''Applied and Environmental Microbiology'', 65(1), 45–52. https://doi.org/10.1128/aem.65.1.45-52.1999</ref>. (3) Plaque assays: serial dilutions of a water sample are applied to a lawn of susceptible host cells and plaques (clearings) are counted. (4) Most probable number (MPN) methods: serial dilution and host infection in multiwell plates.

=== Scale of measurement ===

Each measurement gives a snapshot of viral abundance at a single time point. Time-series measurements reveal viral production and decay rates.

=== Data generated ===

Virus-like particle concentration (VLPs L<sup>-1</sup>); virus-to-bacterium ratio (VBR). Changes in VLP concentration in dilution incubations can estimate viral production rates.

=== Units & currency ===

Units are particles L<sup>-1</sup>. The currency is virus particles.

=== Sample size ===

Typical samples are < 1 L in volume.

=== Repositories & databases ===

== Limitations ==

All particle-counting methods quantify VLPs (virus-like particles) without distinguishing infective from non-infective viruses. Plaque and MPN assays only count viruses infective to the specific host cell line used, missing the majority of marine viral diversity. SYBR Green staining does not distinguish viruses from other small particles with nucleic acid. The assumption that all VLPs are bacteriophage or eukaryotic viruses (vs. gene transfer agents, membrane vesicles) introduces uncertainty.

== Example Applications & Protocols ==

=== Classic examples ===
* Marie et al. (1999) ''Enumeration of marine viruses in culture and natural samples by flow cytometry'' <ref name="Marie1999" />
* Hennes & Suttle (1995) ''Direct counts of viruses in natural waters and laboratory cultures by epifluorescence microscopy'' <ref name="Hennes1995">Hennes, K. P., & Suttle, C. A. (1995). Direct counts of viruses in natural waters and laboratory cultures by epifluorescence microscopy. ''Limnology and Oceanography'', 40(6), 1050–1055. https://doi.org/10.4319/lo.1995.40.6.1050</ref>

=== Recent applications ===
* Brussaard (2004) ''Optimisation of procedures for counting viruses by flow cytometry'' <ref name="Brussaard2004">Brussaard, C. P. D. (2004). Optimisation of procedures for counting viruses by flow cytometry. ''Applied and Environmental Microbiology'', 70(3), 1506–1513. https://doi.org/10.1128/aem.70.3.1506-1513.2004</ref>

=== Common calculations/conversions ===
* Virus-to-bacterium ratio (VBR) = VLP concentration / bacterial cell concentration; typically 10–100 in marine environments.
* Viral production rate (VP, VLPs L<sup>-1</sup> h<sup>-1</sup>) from dilution experiments: VP = ΔVLP / Δt corrected for virus decay.

== References ==

[[Category:Main Pages|Model types]]

Quantification of virus particles - Revision history