Evolutionary Dynamics of Mexican Lineage H5N2 Avian Influenza Viruses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Virus Isolation and Genome Sequencing
2.2. Nucleotide Sequences Used in the Study
2.3. Sequence Analyses
2.4. Intravenous Pathogenicity Index of 2016–2019 Mexican H5N2 AIVs
2.5. Analysis of Selection Pressure
2.6. 3D Structural Analyses
3. Results
3.1. Origins of the Mexican Lineage H5N2 AIV
3.2. The Evolutionary Rate of Mexican Lineage H5N2 AIV
3.3. Protein-Level Evolution and Selection Analysis of Mexican Lineage H5N2 AIVs
3.4. Estimate of Reassortment
3.5. Diversity of the Mexican Lineage H5N2 AIV and HA Cleavage Sites
3.6. Antigenic Evolution of H5N2 AIVs in Mexico
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Segment | Substitution Rate (Subs/Site/Year) | tMRCA (Year) | ||
---|---|---|---|---|
Mean (×10−3) | 95% HPD (×10−3) | Mean | 95% HPD (×10−3) | |
PB2 | 4.32 | 4.01–4.64 | 1990.80 | 1988.88–1992.34 |
PB1 | 3.79 | 3.56–4.04 | 1991.15 | 1989.03–1992.62 |
PA | 3.80 | 3.52–4.06 | 1990.75 | 1988.30–1992.66 |
HA | 5.69 | 5.32–6.06 | 1990.27 | 1987.92–1992.21 |
NP | 3.78 | 3.50–4.08 | 1990.38 | 1987.08–1992.54 |
NA | 5.49 | 5.09–5.91 | 1991.35 | 1988.04–1993.22 |
MP | 3.59 | 3.27–3.89 | 1990.33 | 1987.43–1992.69 |
NS | 4.43 | 4.10–4.76 | 1990.97 | 1988.83–1992.73 |
Gene | Codon Position | SLAC | FUBAR | MEME | |||
---|---|---|---|---|---|---|---|
dN-dS | p-Value | dN-dS | Posterior Probability | p-Value | Number of Branches under Episodic Selection | ||
PB2 | 191 | 1.68 | 0.90 | ||||
PB1 | 296 | 0.00 | 1 | ||||
746 | 2.49 | 0.09 | 1.59 | 0.91 | |||
757 | 0.00 | 1 | |||||
PA | 210 | 3.56 | 0.08 | ||||
489 | 5.02 | 0.05 | 5.91 | 0.98 | 0.00 | 12 | |
PA-X | 193 | 3.48 | 0.08 | 2.11 | 0.98 | ||
216 | 3.32 | 0.06 | 1.91 | 0.97 | |||
218 | 2.85 | 0.09 | 1.57 | 0.95 | |||
221 | 2.74 | 0.09 | |||||
H5 | 88 (72) * | 2.44 | 0.06 | 2.06 | 0.97 | ||
139 (123) | 3.25 | 0.01 | 2.19 | 0.99 | 0.00 | 9 | |
153 (137) | 5.09 | 0.00 | 6.33 | 1.00 | 0.00 | 5 | |
171 (155) | 4.41 | 0.00 | 3.59 | 0.99 | 0.00 | 7 | |
174 (158) | 0.00 | 11 | |||||
194 (178) | 2.54 | 0.07 | 2.00 | 0.95 | |||
197 (181) | 2.96 | 0.04 | 1.94 | 0.95 | |||
201 (185) | 0.00 | 2 | |||||
202 (186) | 0.00 | 4 | |||||
210 (194) | 4.96 | 0.01 | 5.20 | 0.97 | 0.00 | 5 | |
286 (270) | 2.16 | 0.08 | 1.44 | 0.92 | |||
392 (376) | 2.43 | 0.06 | 1.91 | 0.96 | |||
NP | 452 | 3.44 | 0.07 | 2.47 | 0.95 | ||
N2 | 43 | 2.61 | 0.08 | 1.75 | 0.97 | ||
58 | 3.55 | 0.06 | |||||
362 | 0.00 | 1 | |||||
449 | 0.00 | 3 | |||||
M2 | 13 | 2.49 | 0.98 | ||||
20 | 1.63 | 0.94 | |||||
28 | 4.81 | 0.95 | |||||
89 | 1.83 | 0.94 | |||||
NS1 | 63 | 3.04 | 0.06 | 2.57 | 0.97 | ||
64 | 1.72 | 0.92 | |||||
176 | 2.20 | 0.93 | |||||
205 | 1.81 | 0.94 | |||||
210 | 2.60 | 0.08 | 2.11 | 0.96 | |||
215 | 4.24 | 0.02 | 4.94 | 0.98 | 0.01 | 6 | |
221 | 2.68 | 0.95 | |||||
226 | 2.17 | 0.94 | |||||
NS2 | 14 | 3.58 | 0.96 | ||||
44 | 2.74 | 0.92 |
Amino Acid Position a | Structural Location b | Sequons c | Percentage of Isolates (%) |
---|---|---|---|
10 | stalk | NNST | 99.5 |
23 | stalk | NVTV | 99.5 |
45 | VED | NGTK | 1.9 |
54 | VED | NCSV | 2.4 |
72 | VED | NVSE | 1.4 |
84 | VED | NPSN | 53.3 |
126 | RBD | NASA | 5.7 |
NASS | 67.1 | ||
138 | RBD | NGSS | 0.5 |
161 | RBD | NRTY | 0.5 |
163 | RBD | NYTN | 81.9 |
165 | RBD | NNTN | 14.3 |
193 | RBD | NPST | 1.0 |
NPTT | 0.5 | ||
236 | RBD | NDSI | 99.5 |
275 | stalk | NATC | 1.4 |
286 | stalk | NSSL | 79.5 |
NSSM | 14.3 | ||
NTSM | 2.9 | ||
319 | stalk | NVSQ | 0.5 |
480 (484) | stalk | NGTY | 100.0 |
539 (543) | CD | NGSL | 100.0 |
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Xu, W.; Navarro-López, R.; Solis-Hernandez, M.; Liljehult-Fuentes, F.; Molina-Montiel, M.; Lagunas-Ayala, M.; Rocha-Martinez, M.; Ferrara-Tijera, E.; Pérez de la Rosa, J.; Berhane, Y. Evolutionary Dynamics of Mexican Lineage H5N2 Avian Influenza Viruses. Viruses 2022, 14, 958. https://doi.org/10.3390/v14050958
Xu W, Navarro-López R, Solis-Hernandez M, Liljehult-Fuentes F, Molina-Montiel M, Lagunas-Ayala M, Rocha-Martinez M, Ferrara-Tijera E, Pérez de la Rosa J, Berhane Y. Evolutionary Dynamics of Mexican Lineage H5N2 Avian Influenza Viruses. Viruses. 2022; 14(5):958. https://doi.org/10.3390/v14050958
Chicago/Turabian StyleXu, Wanhong, Roberto Navarro-López, Mario Solis-Hernandez, Francisco Liljehult-Fuentes, Miguel Molina-Montiel, María Lagunas-Ayala, Marisol Rocha-Martinez, Eduardo Ferrara-Tijera, Juan Pérez de la Rosa, and Yohannes Berhane. 2022. "Evolutionary Dynamics of Mexican Lineage H5N2 Avian Influenza Viruses" Viruses 14, no. 5: 958. https://doi.org/10.3390/v14050958
APA StyleXu, W., Navarro-López, R., Solis-Hernandez, M., Liljehult-Fuentes, F., Molina-Montiel, M., Lagunas-Ayala, M., Rocha-Martinez, M., Ferrara-Tijera, E., Pérez de la Rosa, J., & Berhane, Y. (2022). Evolutionary Dynamics of Mexican Lineage H5N2 Avian Influenza Viruses. Viruses, 14(5), 958. https://doi.org/10.3390/v14050958