Towards an integrative view of virus phenotypes

DeLong, John P.; Al-Sammak, Maitham Ahmed; Al-Ameeli, Zeina; Dunigan, David D.; Edwards, Kyle F.; Fuhrmann, Jeffry J.; Gleghorn, Jason P.; Li, Hanqun; Haramoto, Kona; Harrison, Amelia O.; Marston, Marcia F.; Rm, Moore; Polson, Shawn W.; Ferrell, Barbra D.; Salsbery, Miranda E.; Schvarcz, Christopher R.; Shirazi, Jasmine; Steward, Grieg F.; Etten, James L. Van; Wommack, K. Eric

doi:10.1038/s41579-021-00612-w

Cited by 21 publications

(29 citation statements)

References 117 publications

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“…The traits we have measured include genome, virion, and virocell performance traits (DeLong et al ., 2022) – we focus on their performance aspects here. The virion and virocell phenotypes were probably mediated by interactions between the viral genotype, the host genotype, and the environment (G V x G H x E interactions), which should be kept in mind when comparing traits between groups and with other studies.…”

Section: Discussionmentioning

confidence: 99%

“…In future, combining trait data with genomic data (Jeanniard et al ., 2013; e.g. Rodrigues et al ., 2022) could allow the creation of a genotype-to-phenotype map to explore chlorovirus evolution (DeLong et al ., 2022).…”

Section: Discussionmentioning

confidence: 99%

“…To understand these effects, it is essential to study viral life histories. Viral life histories are made up of life cycle or ‘performance’ traits such as adsorption rate, lysogeny probability, burst size, and decay rate (performance sensu DeLong et al ., 2022). The values of these traits determine a virus’ population dynamics and ability to suppress the host population, and thus its impact on the broader ecosystem (Weitz, 2016; Horas et al ., 2018).…”

Section: Introductionmentioning

confidence: 99%

“…Measuring life cycle traits requires either microscopic resolution (e.g. Timm & Yin, 2012; Vincent et al ., 2021; DeLong et al ., 2022), which is challenging, or tracking virus concentrations over time (Hiatt, 1964; Hyman & Abedon, 2009), which is labor-intensive when applied to multiple strains. Most studies of multiple (> 3) viruses analyze the diversity within a host species (Baudoux & Brussaard, 2005; De Paepe & Taddei, 2006; Stenholm et al ., 2008; Kahn Mirzaei & Nilsson, 2015), or assemble information within viral ecotypes (Kukkaro & Bamford, 2009; Mojica & Brussaard, 2014; Jurczak-Kurek et al ., 2016; Edwards & Steward, 2018), and most of these focus on a subset of the life cycle traits (an excellent exception is Ceyssens et al ., 2011).…”

Section: Introductionmentioning

confidence: 99%

“…Most studies of multiple (> 3) viruses analyze the diversity within a host species (Baudoux & Brussaard, 2005; De Paepe & Taddei, 2006; Stenholm et al ., 2008; Kahn Mirzaei & Nilsson, 2015), or assemble information within viral ecotypes (Kukkaro & Bamford, 2009; Mojica & Brussaard, 2014; Jurczak-Kurek et al ., 2016; Edwards & Steward, 2018), and most of these focus on a subset of the life cycle traits (an excellent exception is Ceyssens et al ., 2011). As a result, there is a growing information gap between our understanding of viral genetic diversity and the phenotypes that are necessary to parameterize epidemiological models and predict evolutionary responses (DeLong et al ., 2022).…”

Section: Introductionmentioning

confidence: 99%

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High life history diversity within a single genus of phytoplankton viruses

Lievens

Agarkova

Dunigan

et al. 2022

Preprint

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Microbial viruses affect the ecology and evolution of every environment on earth. Although these effects can play out on a grand scale, to understand them we need to zoom in to virus' life cycle traits. The values of these traits determine a virus' effect on the host population, the trait diversity provides the material for natural selection, and trade-offs between the traits are expected to constrain virus' evolutionary potential. However, due to the difficulty involved in measuring viral life history phenotypes, there are not many studies that characterize their diversity within clades of viruses. In this study, we quantified the life history of 35 chloroviruses from three host range groups (NC64A, Osy, and SAG viruses). We developed methods to efficiently measure adsorption rate, depolarization probability, lysis probability, lysis time, burst size, specific infectivity, and decay. The trait estimates varied between 5 and 75-fold across all the virus strains, with most traits varying substantially both within and across groups. We then used our largest virus group, the NC64A viruses (n = 20), to look for correlations that could signal trade-offs between traits. We found that viruses with high depolarization probabilities also had higher burst sizes, but lower lysis probabilities once depolarized. These correlations were strong, but their mechanistic underpinnings are unclear. We also found a strong correlation between growth rate and survival in the NC64A viruses. Finally, we discovered biphasic or 'tailing' decay in all the chlorovirus groups. The nature and diversity of these traits has large implications for the ecology and evolutionary potential of the chloroviruses, and confirm the importance of studying viral life cycle traits.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

High life history diversity within a single genus of phytoplankton viruses

Lievens

Agarkova

Dunigan

et al. 2022

Preprint

Self Cite

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Understanding viruses and viral infections by biophotonic methods

Ramoji

Pahlow

Pistiki

et al. 2022

Transl Biophotonics

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In the last few decades outbreaks of viral infections have often challenged the world‐wide health infrastructure and caused a significant financial burden as well as human suffering despite progress in diagnostic technologies. The recent outbreaks of the Ebola virus in the African continent, the Zika virus in the American continent, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), influenza A and lately severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) viral infections have repeatedly highlighted the importance of technological advancement enabling a better understanding of virions. In this review, we systematically discuss different aspects of virions and how their properties and functions can be studied using different light‐based technologies. We focus on virion classification, detection and interactions with the host's immune system. Further, the potential of advanced biophotonic methods, for example, Raman, infrared reflection, absorption and fluorescence spectroscopy, advanced microscopic techniques and biosensor‐based approaches for diagnosing viral infections, investigating therapeutics and vaccine development are described. Although significant advancements have already been made in photonic technologies, which even enable visualizing virion‐host interactions on single‐cell level, the continuous evolution of viruses demands further progress in biophotonic solutions for fast, affordable and robust health monitoring devices for screening viral infections.

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