Comparative Analysis of HaSNPV-AC53 and Derived Strains
Abstract
:1. Introduction
2. Materials and Methods
2.1. Virus Source and Passage
2.2. Test for Latent Virus
2.3. Strain Isolation by Passage and Selection in Tissue Culture
2.4. DNA Extraction, Next Generation Sequencing Library Preparation, Sequencing and Genome Assembly
2.5. Sequence Analysis and Maximum-Likelihood Estimation (MLE)
3. Results
3.1. Test for Latent Virus
3.2. Strain Isolation
3.3. Sequence Analysis
3.4. Maximum Likelihood Estimation
4. Discussion
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
Script Availability
References
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Strain | Time (h) Post-Infection (pi) | First Round Isolation Method |
---|---|---|
AC53-C1 | 48 and 48 | Agar Overlay |
AC53-C5 | 48 and 48 | Agar Overlay |
AC53-C6 | 48 and 48 | Agar Overlay |
AC53-C9 | 48 and 48 | Agar Overlay |
AC53-C3 | 72 and 72 | Agar Overlay |
AC53-T2 | 48 and 48 | Tissue Culture—No Overlay |
AC53-T4.1 * | 72 and 96 | Tissue Culture—No Overlay |
AC53-T4.2 * | 72 and 96 | Tissue Culture—No Overlay |
AC53-T5 | 72 and 120 | Tissue Culture—No Overlay |
Common Name | Genbank Accession | Sequence Length (bp) | Nucleotide Identity to AC53 (%) | Country/Region of Origin |
---|---|---|---|---|
HaSNPV-AC53-C1 | KU738896 | 130,460 | 99.624 | Australia |
HaSNPV-AC53-C5 | KU738898 | 130,439 | 99.600 | Australia |
HaSNPV-AC53-C6 | KU738899 | 130,435 | 99.601 | Australia |
HaSNPV-AC53-T4.1 | KU738902 | 130,440 | 99.602 | Australia |
HaSNPV-AC53-T5 | KU738904 | 130,442 | 99.603 | Australia |
HaSNPV-AC53-C9 | KU738897 | 130,437 | 99.599 | Australia |
HaSNPV-AC53-T2 | KU738901 | 130,440 | 99.596 | Australia |
HaSNPV-AC53-T4.2 | KU738896 | 130,443 | 99.530 | Australia |
HaSNPV-AC53-C3 | KU738897 | 130,437 | 99.595 | Australia |
HaSNPV-H25EA1 | KJ922128 | 130,436 | 99.423 | Australia |
HzSNPV-HS18 | KJ004000 | 130,890 | 99.220 | Unknown—Sequenced in Russia |
HzSNPV-F16 (Elcar-derived) | AF334030 | 130,869 | 99.208 | USA—Sequenced in China |
HzSNPV-Br/South | KM596835 | 129,694 | 98.277 | Brazil |
HaSNPV-NNg1 | AP010907 | 132,425 | 96.203 | Kenya |
HaSNPV-LB1 | KJ701029 | 131,966 | 96.012 | Iberia |
HaSNPV-SP1A | KJ701032 | 132,481 | 95.961 | Iberia |
HaSNPV-SP1B | KJ701033 | 132,265 | 95.810 | Iberia |
HaSNPV-LB3 | KJ701030 | 130,949 | 95.799 | Iberia |
HaSNPV-LB6 | KJ701031 | 130,992 | 95.798 | Iberia |
HaSNPV-C1 | AF303045 | 130,759 | 95.353 | China |
HaSNPV-AU | JN584482 | 130,992 | 94.860 | Australia—Sequenced in China |
HaSNPV-G4 | AF271059 | 131,405 | 94.442 | China |
ORF | Protein | AC53-C1 | AC53-C3 | AC53-C5 | AC53-C6 | AC53-C9 | AC53-T2 | AC53-T4.1 | AC53-T4.2 | AC53-T5 | Notes | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
AA | N | AA | N | AA | N | AA | N | AA | N | AA | N | AA | N | AA | N | AA | N | |||
4 | HOAR | 95.6 | 95.7 | 95.8 | 96.1 | 96.9 | 97.1 | 96.8 | 96.9 | 96.9 | 96.9 | 96.7 | 96.9 | 96.7 | 96.9 | 96.9 | 96.9 | 96.7 | 96.9 | |
5 | 34.9 | 97.2 | 98.3 | 98.9 | 34.9 | 97.2 | 34.9 | 97.2 | 34.9 | 97.2 | 34.9 | 97.2 | 34.9 | 97.2 | 34.9 | 97.2 | 34.9 | 97.2 | AC53 and AC53-C3 have identical length | |
6 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | 99.3 | ||
7 | 94.1 | 99.3 | 94.1 | 99.3 | 94.1 | 99.3 | 94.1 | 99.3 | 94.1 | 99.3 | 94.1 | 99.3 | 94.1 | 99.3 | 94.1 | 99.3 | 94.1 | 99.3 | AC53 is 85 bp shorter | |
Hr1 | N.A | 99.7 | N.A | 99.7 | N.A | 99.7 | N.A | 99.8 | N.A | 99.8 | N.A | 99.7 | N.A | 99.7 | N.A | 99.8 | N.A | 99.7 | ||
Hr2 | N.A | 95.5 | N.A | 95.2 | N.A | 95.2 | N.A | 95.2 | N.A | 95.3 | N.A | 95.2 | N.A | 95.2 | N.A | 95.2 | N.A | 95.2 | ||
Hypothetical ORF | Hypothetical Protein | 70.7 | 98.0 | 70.7 | 98.0 | 70.7 | 98.0 | 70.7 | 98.0 | 70.7 | 98.0 | 70.7 | 98.0 | 70.7 | 98.0 | 70.7 | 98.0 | 70.7 | 98.0 | AC53 is 24 bp shorter |
59 | BRO-A | 90.9 | 92.1 | 90.9 | 92.1 | 90.9 | 92.1 | 90.9 | 92.1 | 90.9 | 92.1 | 91.3 | 92.1 | 90.9 | 92.1 | 90.9 | 92.1 | 90.9 | 92.1 | |
60 | BRO-B | 90.4 | 94.0 | 90.4 | 94.0 | 90.4 | 94.0 | 90.4 | 94.0 | 90.4 | 94.0 | 90.4 | 94.0 | 90.4 | 94.0 | 90.4 | 94.0 | 90.4 | 94.0 | |
Hr3 | N.A | 99.6 | N.A | 99.6 | N.A | 99.6 | N.A | 99.6 | N.A | 99.6 | N.A | 99.69 | N.A | 99.6 | N.A | 99.8 | N.A | 99.6 | ||
61 | 80.0 | 86.9 | 86.8 | 86.9 | 80.0 | 86.9 | 80.0 | 86.9 | 80.0 | 86.9 | 80.0 | 86.9 | 80.0 | 86.9 | 80.0 | 86.9 | 80.0 | 86.9 | AC53 is 41 bp longer | |
68 | DNA polymerase | 100 | 100 | 99.9 | 99.9 | 99.9 | 99.9 | 100 | 100 | 100 | 100 | 99.9 | 99.9 | 100 | 100 | 100 | 100 | 100 | 100 | |
78a/78b (ORF78 in all other strains) | 100 | 100 | 100 | 100 | 100 | 100 | 76.3 | 99.4 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | Split in two with AC53-C6 | |
Hr4 | N.A | 99.5 | N.A | 99.0 | N.A | 99.0 | N.A | 99.0 | N.A | 99.0 | N.A | 99.0 | N.A | 99.0 | N.A | 99.0 | N.A | 99.0 | ||
Hr5 | N.A | 99.3 | N.A | 99.1 | N.A | 99.1 | N.A | 99.5 | N.A | 99.2 | N.A | 99.1 | N.A | 99.4 | N.A | 99.1 | N.A | 99.4 | ||
126 | 38.7K | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 99.7 | 99.4 | 100 | 100 | 100 | 99.8 | 100 | 100 | |
128a/128b (ORF128 in all other strains) | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 23.2 | 87.6 | 100 | 100 | Split in two with AC53-T4.2 | |
133 | PKIP-1 | 100 | 100 | 100 | 99.8 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | |
137 | 97.2 | 99.3 | 97.2 | 99.3 | 97.2 | 99.3 | 97.2 | 99.3 | 97.2 | 99.3 | 97.2 | 99.3 | 97.2 | 99.3 | 97.2 | 99.3 | 97.2 | 99.3 | ||
Total regions with sequence polymorphisms | 9 | 14 | 10 | 16 | 10 | 15 | 10 | 15 | 8 | 14 | 11 | 16 | 9 | 14 | 10 | 16 | 9 | 14 |
ORF/Region | Nucleotide Similarity and Clusters within Derived Strains | Amino Acid Similarity and Clusters within Derived Strains |
---|---|---|
HOAR | - AC53-T4.1, AC53-T5 = 100% | - AC53-T4.1 and AC53-T5 = 100% |
- AC53-C6, AC53-C9, AC53-T4.2 = 100% | - AC53-C6, AC53-C9 ,AC53-T4.2 = 100% | |
- Remaining 4 strains all different at 96.7% to 99.9% | - Remaining 4 strains all different at 95.8% to 99.8% | |
ORF5 * | - AC53-C3 = 96.1% | - AC53-C3 = 33.3% |
- Remaining strains all identical | - Remaining strains all identical | |
BRO-A | - AC53-T2 = 99.9% | - AC53-T2 = 99.5% |
- Remaining strains all identical | - Remaining strains all identical | |
DNA-Polymerase | - AC53-T5, AC53-T4.2, AC53-T4.1, AC53-C9, AC53-C6, AC53-C1 = 100% | - AC53-C3, AC53-C5, AC53-T2 = 100% |
- AC53-C5, AC53-C3 = 100% | - AC53-T5, AC53-T4.2, AC53-T4.1, AC53-C9, AC53-C6 | |
- AC53-T2 = 99.9% | - AC53-C1 = 100% | |
ORF78/ORF78a and 78b in AC53-C6 | - AC53-C6 = 99.4% | - AC53-C6 = 77.9% |
- Remaining strains all identical | - Remaining strains all identical | |
38.7K Protein | - AC53-T2 = 99.4% to other 7 strains and 99.6% to AC53-T4.2 | - AC53-T2 = 99.7% |
- AC53-T4.2 = 99.8% to other 7 strains | - Remaining 8 strains all identical | |
- Remaining 7 strains all identical | ||
ORF128/ORF128a and 128b in AC53-T4.2 | - AC53-T4.2 = 87.6% | - AC53-T4.2 = 23.2% |
- Remaining strains all identical | - Remaining strains all identical | |
PKIP-1 | - AC53-C3 = 99.8% | - All strains = 100% |
- Remaining strains all identical | ||
Hr1 | - AC53-T4.2, AC53-C9, AC53-C6 = 100% | - Not Applicable |
- AC53-T5, AC53-T4.1, AC53-T2, AC53-C5, AC53-C3, AC53-C1 = 100% | ||
- 99.9% when both groups compared | ||
Hr2 | - AC53-C6, AC53-T4.1 = 100% | - Not Applicable |
- Remaining strains all identical | ||
Hr3 | - AC53-T4.2 = 99.8% | - Not Applicable |
- Remaining strains all identical | ||
Hr4 | - AC53-C1 = 99.2% | - Not Applicable |
- Remaining strains all identical | ||
Hr5 | - AC53-T2, AC53-C5, AC53-C3 = 100% | - Not Applicable |
- Remaining strains all identical |
© 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
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Noune, C.; Hauxwell, C. Comparative Analysis of HaSNPV-AC53 and Derived Strains. Viruses 2016, 8, 280. https://doi.org/10.3390/v8110280
Noune C, Hauxwell C. Comparative Analysis of HaSNPV-AC53 and Derived Strains. Viruses. 2016; 8(11):280. https://doi.org/10.3390/v8110280
Chicago/Turabian StyleNoune, Christopher, and Caroline Hauxwell. 2016. "Comparative Analysis of HaSNPV-AC53 and Derived Strains" Viruses 8, no. 11: 280. https://doi.org/10.3390/v8110280