Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Culture
2.2. RNA Extraction and Sequencing
2.3. In Vivo Studies
2.4. Bioinformatic Analyses
- SNP density: (where ind[y] is 1 if y is true and 0 otherwise)
- Pairwise nucleotide diversity:
- Entropy:
- Tajima’s D:
3. Results
3.1. Samples and Read Depth
3.2. Overall Genetic Diversity Show Higher Diversity in the In Vivo Samples
3.3. An Excess of Low-Frequency Variants is Compatible with an Exponential Growth Rate within Host/Culture
3.4. Genetic Diversity along the Genome Shows Regions of High Diversity and/or Hypermutability
3.5. The Site Frequency Spectrum (SFS) Gives Clues about Evolutionary Events Occurring within Host
3.6. Looking for Signatures of Selection: Non-Synonymous, Synonymous and Non-Coding Variants
3.6.1. Ratios of Polymorphism within-Host at Functional Versus Non-Functional Positions
3.6.2. The Patterns of Polymorphism within-Host Versus the Divergence between-Host Are not Always Correlated
3.6.3. Contrasting the Patterns of Polymorphism within-Host Versus the Divergence between-Host at Functional Versus Non-Functional Positions: Differential Selective Patterns at Different Stages
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Samples | Total Number of Sequenced High Quality Nucleotides | Number of Bases with Read Depth ≥100 | ||
---|---|---|---|---|
Host | Virus | Replicate | ||
in vivo Leghorn (susceptible line) | LaSota | 1 | 7,863,831 | 7947 |
2 | 40,862,546 | 10,853 | ||
3 | 24,478,520 | 8116 | ||
in vivo Fayoumi (resistant line) | 1 | 7,209,555 | 7961 | |
2 | 2,260,242 | 7387 | ||
in vitro Chicken embryo fibroblast (CEF) cells | LaSota | 1 | 513,645,350 | 15,169 |
2 | 489,575,827 | 15,169 | ||
3 | 493,067,864 | 15,169 | ||
Herts/33 | 1 | 2,297,752,521 | 15,162 | |
2 | 2,538,051,612 | 15,169 | ||
3 | 2,158,838,655 | 15,163 |
Gene | NP | P | M | F | HN | HN |
---|---|---|---|---|---|---|
Feature | Peak in polymorphism | Correlated patterns pol-div. | Generally low polymorphisms | Dip in divergence | 1st peak in divergence | 2nd peak in divergence |
Genomic position (±250 bp) | 683–684 (leghorn1) | Whole gene (3290–4384) | 5018–5019 | 6589–6593 | 7219–7220 |
Protein | NP | P | M | F | F | HN | HN |
---|---|---|---|---|---|---|---|
Feature | dip | peak | dip | 1st peak | 2nd peak | 1st peak | 2nd peak |
Location (dark gray in Figure 8) | 600–900 | 2300–2700 | 3550–3800 | 4750–4850 | 5200–5350 | 6600–6750 | 7100–7400 |
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Jadhav, A.; Zhao, L.; Liu, W.; Ding, C.; Nair, V.; Ramos-Onsins, S.E.; Ferretti, L. Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections. Viruses 2020, 12, 1305. https://doi.org/10.3390/v12111305
Jadhav A, Zhao L, Liu W, Ding C, Nair V, Ramos-Onsins SE, Ferretti L. Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections. Viruses. 2020; 12(11):1305. https://doi.org/10.3390/v12111305
Chicago/Turabian StyleJadhav, Archana, Lele Zhao, Weiwei Liu, Chan Ding, Venugopal Nair, Sebastian E. Ramos-Onsins, and Luca Ferretti. 2020. "Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections" Viruses 12, no. 11: 1305. https://doi.org/10.3390/v12111305