The Canine Morbillivirus Strain Associated with An Epizootic in Caspian Seals Provides New Insights into the Evolutionary History of this Virus
Abstract
:1. Introduction
2. Materials and Methods
2.1. Tissue Samples
2.2. Sample Processing
2.3. Generation of Full-Length Genome
2.4. Phylogenetic Analyses
3. Results
3.1. Identification of a Novel CDV Clade in Caspian Seals
3.2. Divergence Dates between CDV Clades
3.3. Evolutionary Rate of CDV
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Clade | Strain Variant | Stranding Year | Location | Host | Sample Material | Coverage | GenBank Accession No. |
---|---|---|---|---|---|---|---|
Caspian | PC00-46 | 2000 | Kazakhstan | Caspian seal | Kidney | 393x | MN267064 |
Caspian | PC00-20 | 2000 | Kazakhstan | Caspian seal | Kidney | 547x | -- |
Caspian | PC00-20 | 2000 | Kazakhstan | Caspian seal | Lung | 9149x | MN267065 |
Caspian | PC00-21 | 2000 | Azerbaijan | Caspian seal | Lung | 33184x | MN267066 |
Caspian | PC00-21 | 2000 | Azerbaijan | Caspian seal | Kidney | 0.3x | -- |
Arctic | PS88-428 | 1988 | Russia | Baikal seal | Lung | 2572x | MN267063 |
Arctic | PS88-428 | 1988 | Russia | Baikal seal | Spleen | 247x | -- |
Europe-1 | S466 | 2015 | Germany | Raccoon | Lung | 19505x | MN267062 |
Europe-1 | S460 | 2015 | Germany | Raccoon | Lung | 9922x | MN267060 |
Europe-1 | S272 | 2016 | Germany | Fox | Tonsils | 157x | MN267061 |
Protein | PC00-46/20/21 (Caspian seal) | PS88-428 (Baikal seal) | S460/S466/S272 (Europe-1) | |
---|---|---|---|---|
Nucleocapsid | N65S | A140V | D151N | |
D135N | P/L432S | |||
S439F | T/A/S434V | |||
G458E | R438S | |||
Y459H | L/F/P/V456S | |||
Y/F/H471P | V463A | |||
E/G467K | ||||
Phosphoprotein | I29V | P223S | H/Y75D | E54D |
N/D46S | S238L | D206E | Q102H | |
T/I/A48G | S254P | G/S418N | T209I | |
M/V/K51I | V272A | D443N | ||
K/R/E68T | A458P | |||
N/S138D | ||||
Matrix | No unique changes | No unique changes | S202L | |
Fusion | K/N/E/R3G | R/K73G | V/A/T32I | I/T/S/V30A |
E/K7T | S/L74P | R/M/G65I | I/T33V/A | |
Q/R22H | V/I/F87T | S/T91P | V/I/D57T | |
V/A/T32I | V/I94A | I/T/V110F | A/G85C | |
Q/H/R/L43K | I/L124F | I515M | ||
H/R/Y47D | P161S | N517S | ||
T/I/A52K | K211R | P613L | ||
C/R67H | P/L212S | |||
Q69H | D/A644N | |||
A/T70I | ||||
Hemagglutinin | P35S | T360I | A191V | S311P |
K/R161N | E379K | R/K197E | D/N313S | |
L175I | S394A | D571G | V334M | |
G/R177E | I/T/V417A | M362V | ||
G/D/A178S | E/D441K | M/V389I | ||
V/I/S198G | S/P447F | Q516R | ||
P/S200L | G488R | T590I | ||
I210V | S497P | R/C/H/S597Y | ||
D/N237Y | R/I519K | |||
T/S245A | E/D560N | |||
T268I | D/N584T | |||
Y/S305H | K/N606S | |||
N/S/D/R309K | ||||
Large | A32S | K1229R | N319T | V6I |
N/S37R | N/H1391I | R699K | C/R65Y | |
T43A | S/I/V1392T | V/I975M | V85M | |
R47C | V1445I | V/A256G | ||
I66V | Q/R1701S | D318V | ||
S/A/P252T | S/P1702L | Y400F | ||
M/I385L | S1995T | T/A/S/I622G | ||
R/C/Y/S/W611H | S2023G | D717N | ||
K/R615Q | N2141H | I917V | ||
L1179I | F1718L | |||
N/T1776K | ||||
I2024M | ||||
L2175V | ||||
Total | 80 changes | 15 changes | 39 changes |
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Jo, W.K.; Peters, M.; Kydyrmanov, A.; van de Bildt, M.W.G.; Kuiken, T.; Osterhaus, A.; Ludlow, M. The Canine Morbillivirus Strain Associated with An Epizootic in Caspian Seals Provides New Insights into the Evolutionary History of this Virus. Viruses 2019, 11, 894. https://doi.org/10.3390/v11100894
Jo WK, Peters M, Kydyrmanov A, van de Bildt MWG, Kuiken T, Osterhaus A, Ludlow M. The Canine Morbillivirus Strain Associated with An Epizootic in Caspian Seals Provides New Insights into the Evolutionary History of this Virus. Viruses. 2019; 11(10):894. https://doi.org/10.3390/v11100894
Chicago/Turabian StyleJo, Wendy K., Martin Peters, Aidyn Kydyrmanov, Marco W. G. van de Bildt, Thijs Kuiken, Albert Osterhaus, and Martin Ludlow. 2019. "The Canine Morbillivirus Strain Associated with An Epizootic in Caspian Seals Provides New Insights into the Evolutionary History of this Virus" Viruses 11, no. 10: 894. https://doi.org/10.3390/v11100894
APA StyleJo, W. K., Peters, M., Kydyrmanov, A., van de Bildt, M. W. G., Kuiken, T., Osterhaus, A., & Ludlow, M. (2019). The Canine Morbillivirus Strain Associated with An Epizootic in Caspian Seals Provides New Insights into the Evolutionary History of this Virus. Viruses, 11(10), 894. https://doi.org/10.3390/v11100894