Molecular Epidemiology of B3 and D8 Measles Viruses through Hemagglutinin Phylogenetic History
Abstract
:1. Introduction
2. Results
2.1. Hemagglutinin Phylogenetic and Sequence Analyses
2.2. Overall Selective Pressure Analyses
2.3. Genotype B3
2.3.1. Phylogenetic Analyses and Molecular Epidemiology
2.3.2. Genetic Drift and Amino Acid Substitutions
2.4. Genotype D8
2.4.1. Phylogenetic Analyses and Molecular Epidemiology
2.4.2. Genetic Drift and Amino Acid Substitutions
2.5. Analysis of the Immune Epitopes
3. Discussion
4. Conclusions
5. Materials and Methods
5.1. Sequencing of the Hemagglutinin Gene
5.2. Phylogenetic Analyses
5.3. Selection Pressure Analyses
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
CDC | Centers for Disease Control and Prevention |
H | Hemagglutinin |
HNE | Hemagglutinating and noose epitope |
LE | Loop epitope |
MV | Measles virus |
MeaNS | Measles Nucleotide Surveillance |
NE | Neutralizing epitope |
n-450 | 450 nucleotides encoding the carboxyl-terminal 150 amino acids of the nucleoprotein |
RBE | Receptor-binding epitope |
SSE | Sugar-shielded epitope |
WHO | World Health Organization |
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Strain | Classification 1 | Case 2 | Vaccination 3 | Origin |
---|---|---|---|---|
B3-2015 | ||||
MVs/Lecco.ITA/44.15 | B3 Niger | Sporadic | Unvaccinated | Imported |
MVs/Pavia.ITA/44.15 | B3 Como | Outbreak | Unvaccinated | Autochthonous |
MVs/Pavia.ITA/44.15/2 | B3 Como | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/45.15 | B3 Como | Sporadic | Unvaccinated | Autochthonous |
MVs/Pavia.ITA/46.15 | B3 Como | Sporadic | Unvaccinated | Autochthonous |
MVs/Lecco.ITA/47.15 | B3 Niger | Sporadic | Vaccinated (1) | Autochthonous |
MVs/Milan.ITA/53.15/2 | B3 Como | Sporadic | Vaccinated (1) | Autochthonous |
MVs/Milan.ITA/53.15/5 | B3 Como | Outbreak | Unvaccinated | Autochthonous |
B3-2016 | ||||
MVs/Milan.ITA/1.16 | B3 Como | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/1.16/2 | B3 Niger | Outbreak | Vaccinated (1) | Autochthonous |
MVs/Milan.ITA/1.16/3 | B3 Como | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/2.16 | B3 Niger | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/3.16/2 | B3 Como | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/3.16 | B3 Como | Outbreak | Vaccinated (2) | Autochthonous |
MVs/Milan.ITA/3.16/4 | B3 Como | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/3.16/6 | B3 Como | Outbreak | Vaccinated (1) | Autochthonous |
MVs/Milan.ITA/6.16/3 | B3 Como | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/7.16 | B3 Como | Outbreak | Vaccinated (1) | Autochthonous |
MVs/Pavia.ITA/08.16 | B3 Niger | Sporadic | Vaccinated (1) | Autochthonous |
B3-2017 | ||||
MVs/Bergamo.ITA/9.17 | B3 Dublin | Outbreak | Unvaccinated | Imported |
MVs/Brescia.ITA/12.17 | B3 Dublin | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/17.17/2 | B3 Dublin | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/21.17/3 | B3 Dublin | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/22.17/4 | B3 Dublin | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/23.17/3 | B3 Dublin | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/23.17/4 | B3 Dublin | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/25.17/12 | B3 Dublin | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/26.17/3 | B3 Dublin | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/38.17 | B3 Dublin | Sporadic | Vaccinated (2) | Autochthonous |
B3-2018 | ||||
MVs/Milan.ITA/8.18/2 | B3 Dublin | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/10.18/2 | B3 Dublin | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/11.18 | B3 Dublin | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/11.18/3 | B3 Dublin | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/13.18/2 | B3 Dublin | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/14.18 | B3 Dublin | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/14.18/2 | B3 Dublin | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/15.18/3 | B3 Ljubjana | Sporadic | Unvaccinated | Imported |
MVs/Milan.ITA/15.18/4 | B3 Dublin | Sporadic | Unvaccinated | Imported |
MVs/Milan.ITA/16.18 | B3 Dublin | Sporadic | Unvaccinated | Autochthonous |
MVs/Brescia.ITA/17.18 | B3 Dublin | Outbreak | Unvaccinated | Autochthonous |
MVs/Como.ITA/16.18 | B3 Ljubjana | Sporadic | Unvaccinated | Autochthonous |
MVs/Como.ITA/17.18 | B3 Ljubjana | Outbreak | Unvaccinated | Autochthonous |
MVs/Como.ITA/18.18 | B3 Ljubjana | Outbreak | Vaccinated (1) | Autochthonous |
MVs/Como.ITA/18.18/2 | B3 Ljubjana | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/24.18/n | B3 Dublin | Outbreak | Vaccinated (2) | Autochthonous |
MVs/Milan.ITA/26.18 | B3 Unnamed 4 | Sporadic | Vaccinated (2) | Imported |
MVs/Milan.ITA/27.18 | B3 Unnamed | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/27.18/2 | B3 Unnamed | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/27.18/4 | B3 Unnamed | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/28.18 | B3 Unnamed | Outbreak | Unvaccinated | Autochthonous |
MVs/MonzaBrianza.ITA/28.18 | B3 Unnamed | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/28.18/2 | B3 Unnamed | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/47.18 | B3 Saint Denis | Outbreak | Unvaccinated | Autochthonous |
D8-2017 | ||||
MVs/Como.ITA/16.17 | D8 Osaka | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/12.17/1 | D8 Osaka | Outbreak | Vaccinated (1) | Autochthonous |
MVs/Milan.ITA/12.17/6 | D8 Osaka | Sporadic | Unvaccinated | Autochthonous |
MVs/MonzaBrianza.ITA/12.17/2 | D8 Osaka | Outbreak | Unvaccinated | Autochthonous |
MVs/Como.ITA/14.17/2 | D8 Osaka | Outbreak | Unvaccinated | Autochthonous |
MVs/Como.ITA/14.17/4 | D8 Osaka | Outbreak | Vaccinated (2) | Autochthonous |
MVs/MonzaBrianza.ITA/15.17/5 | D8 Osaka | Outbreak | Unvaccinated | Autochthonous |
MVs/Como.ITA/17.17/2 | D8 Osaka | Sporadic | Vaccinated (1) | Autochthonous |
MVs/Varese.ITA/21.17 | D8 Osaka | Outbreak | Vaccinated (1) | Autochthonous |
MVs/Milan.ITA/24.17/2 | D8 Osaka | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/24.17/4 | D8 London | Sporadic | Vaccinated (1) | Autochthonous |
MVs/Milan.ITA/24.17/7 | D8 Osaka | Outbreak | Vaccinated (1) | Autochthonous |
MVs/Milan.ITA/25.17/15 | D8 Osaka | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/26.17/2 | D8 Osaka | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/26.17/6 | D8 Osaka | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/26.17 | D8 Osaka | Outbreak | Vaccinated (2) | Autochthonous |
MVs/Milan.ITA/26.17/7 | D8 Osaka | Outbreak | Vaccinated (1) | Autochthonous |
MVs/Milan.ITA/26.17/8 | D8 Osaka | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/26.17/16 | D8 Osaka | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/27.17/5 | D8 London | Outbreak | Vaccinated (2) | Autochthonous |
MVs/Milan.ITA/27.17/19 | D8 Osaka | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/23.17/15 | D8 Osaka | Sporadic | Vaccinated (2) | Autochthonous |
MVs/Lodi.ITA/30.17/2 | D8 London | Outbreak | Vaccinated (1) | Autochthonous |
MVs/Milan.ITA/31.17/3 | D8 Osaka | Outbreak | Vaccinated (2) | Autochthonous |
D8-2018 | ||||
MVs/Milan.ITA/10.18/4 | D8 Unnamed | Sporadic | Unvaccinated | Autochthonous |
MVs/Brescia.ITA/11.18 | D8 Unnamed | Outbreak | Unvaccinated | Imported |
MVs/Brescia.ITA/11.18/2 | D8 Unnamed | Sporadic | Unvaccinated | Autochthonous |
MVs/Brescia.ITA/12.18/2 | D8 Unnamed | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/13.18 | D8 Unnamed | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/15.18 | D8 Unnamed | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/17.18 | D8 Unnamed | Sporadic | Vaccinated (2) | Imported |
MVs/Milan.ITA/18.18 | D8 Unnamed | Sporadic | Unvaccinated | Autochthonous |
MVs/Milan.ITA/14.18/ | D8 Unnamed | Outbreak | Unvaccinated | Autochthonous |
MVs/Milan.ITA/10.18/3 | D8 Unnamed | Sporadic | Vaccinated (1) | Autochthonous |
D8-2019 | ||||
Mvs/Milan.ITA/4.19 | D8 Gir-Somnath | Sporadic | Vaccinated (1) | Imported |
Mvs/Milan.ITA/4.19/3 | D8 Gir-Somnath | Sporadic | Vaccinated (2) | Imported |
Mvs/Milan.ITA/5.19 | D8 Gir-Somnath | Sporadic | Vaccinated (1) | Autochthonous |
Mvs/Milan.ITA/16.19 | D8 Gir-Somnath | Sporadic | Vaccinated (1) | Autochthonous |
Mvs/Milan.ITA/19.19/2 | D8 Gir-Somnath | Outbreak | Unvaccinated | Autochthonous |
Mutation | Overall n (%) 1 | n in Specific Clades/Clusters | Immune Epitope/Recognizing Antibody 2 | PSP 3 |
---|---|---|---|---|
400V | 127 (0.4) | Clade 400V: 126 | HNE | |
178T | 120 (8.9) | Clade 400V: 119 | ||
307I | 123 (9.1) | Clade 400V: 119 | ||
165T | 12 (0.9) | Cluster Niger: 6 | ||
222I | 7 (0.5) | Cluster Niger: 6 | ||
282D | 35 (2.6) | Cluster Niger: 6 | Yes | |
542F | 1 (0.1) | Cluster Niger: 1 | ||
601A | 3 (0.2) | Cluster Niger: 3 | ||
603E | 50 (3.7) | Cluster Niger: 3 Cluster D/L/SD: 1 | ||
605T | 3 (0.2) | Cluster Como: 3 | ||
617K | 5 (0.4) | Cluster Como: 3 | ||
429T | 1 (0.1) | Cluster Como: 1 | ||
71R | 2 (0.1) | Cluster Como: 1 | ||
30P | 3 (0.2) | Cluster Como: 1 | ||
50V | 8 (0.6) | Cluster Unnamed: 7 | ||
192A | 10 (0.7) | Cluster Unnamed: 7 | Ab I-44, BH26 | |
412L | 7 (0.5) | Cluster Unnamed: 7 | ||
355K | 3 (0.2) | Cluster Unnamed: 1 | ||
585I | 52 (3.9) | Cluster D/L/SD: 52 | ||
465S | 1 (0.1) | Cluster D/L/SD: 1 | ||
509E | 1 (0.1) | Cluster D/L/SD: 1 | ||
321F | 1 (0.1) | Cluster D/L/SD: 1 | ||
400A | 1004 (74.5) | Cluster D/L/SD: 1 | HNE | |
445Q | 1 (0.1) | Cluster D/L/SD: 1 | ||
176I | 2 (0.1) | Cluster D/L/SD: 1 |
Mutation | Overall n (%) 1 | n in Specific Clades/Clusters | Immune Epitope/Recognizing Antibody 2 | PSP 3 |
---|---|---|---|---|
400T | 213 (15.8) | Clade 400T: 209 | HNE | |
416D | 951 (70.6) | Clade 400T: 212 | SSE | |
560R | 145 (10.8) | Clade 400T: 123 | ||
174T | 849 (63.0) | Clade 400T: 115 | ||
559V | 131 (9.7) | Clade 400T: 116 | ||
276L | 270 (20.0) | Clade 400T: 111 | ||
428V | 111 (8.2) | Clade 400T: 110 | ||
560K | 1199 (89.0) | Clade 400T: 89 | ||
243E | 91 (6.8) | Clade 400T: 89 | ||
328R | 35 (2.6) | Cluster Unnamed: 10 | ||
247P | 155 (11.5) | Cluster Unnamed: 22 | NE | |
285G | 206 (15.3) | Cluster Gir-Somnath: 1 | ||
375Q | 1 (0.1) | Cluster Gir-Somnath: 1 Cluster London/Osaka: 1 | ||
575K | 68 (5.1) | Cluster Gir-Somnath: 1 | BH26 | Yes |
23T | 1 (0.1) | Cluster London/Osaka: 1 | ||
603R | 4 (0.3) | Cluster London/Osaka: 1 | ||
375R | 6 (0.5) | Cluster London/Osaka: 3 | ||
247L | 23 (1.7) | Cluster London/Osaka: 14 | NE | |
145K | 8 (0.6) | Cluster London/Osaka: 7 |
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Bianchi, S.; Canuti, M.; Ciceri, G.; Gori, M.; Colzani, D.; Dura, M.; Pennati, B.M.; Baggieri, M.; Magurano, F.; Tanzi, E.; et al. Molecular Epidemiology of B3 and D8 Measles Viruses through Hemagglutinin Phylogenetic History. Int. J. Mol. Sci. 2020, 21, 4435. https://doi.org/10.3390/ijms21124435
Bianchi S, Canuti M, Ciceri G, Gori M, Colzani D, Dura M, Pennati BM, Baggieri M, Magurano F, Tanzi E, et al. Molecular Epidemiology of B3 and D8 Measles Viruses through Hemagglutinin Phylogenetic History. International Journal of Molecular Sciences. 2020; 21(12):4435. https://doi.org/10.3390/ijms21124435
Chicago/Turabian StyleBianchi, Silvia, Marta Canuti, Giulia Ciceri, Maria Gori, Daniela Colzani, Marco Dura, Beatrice Marina Pennati, Melissa Baggieri, Fabio Magurano, Elisabetta Tanzi, and et al. 2020. "Molecular Epidemiology of B3 and D8 Measles Viruses through Hemagglutinin Phylogenetic History" International Journal of Molecular Sciences 21, no. 12: 4435. https://doi.org/10.3390/ijms21124435