Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains
Abstract
:1. Introduction
2. Materials and Methods
2.1. Clinical Specimens and HMPV Isolation
2.2. Full-Genome Analysis of HMPV
2.3. Maximum Likelihood Phylogenies
2.4. Molecular Clock Phylogenies
2.5. Ethics Statement
3. Results
3.1. Isolation of HMPV A2b111nt-dup Strains and the Phylogenetic Relationship among HMPV Strains
3.2. Genetic Distances between HMPV Subtypes
3.3. Evolutional Analysis of HMPV
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Strain Name | Isolation Year | Isolation Cell | 111nt-dup |
---|---|---|---|
HMPV/Yokohama/P8918/2017 | 2017 | VeroE6/TMPRSS2 | + |
HMPV/Yokohama/P8943/2017 | 2017 | VeroE6/TMPRSS2 | + |
HMPV/Yokohama/P8945/2017 | 2017 | VeroE6/TMPRSS2 | + |
HMPV/Yokohama/P9299/2018 | 2018 | VeroE6/TMPRSS2 | + |
HMPV/Yokohama/P9321/2018 | 2018 | VeroE6/TMPRSS2 | + |
HMPV/Yokohama/P9372/2018 | 2018 | VeroE6/TMPRSS2 | + |
HMPV/Yokohama/P9416/2018 | 2018 | VeroE6/TMPRSS2 | + |
HMPV/Yokohama/P9506/2018 | 2018 | VeroE6/TMPRSS2 | + |
HMPV/Yokohama/P9507/2018 | 2018 | VeroE6/TMPRSS2 | + |
HMPV/Yokohama/P9510/2018 | 2018 | VeroE6/TMPRSS2 | + |
HMPV/Yokohama/P9547/2018 | 2018 | VeroE6/TMPRSS2 | + |
- | Genetic Distance (p-Value) * | - | - | - | ||
---|---|---|---|---|---|---|
Subtype | A1 | A2a | A2b1 | A2b2 | B1 | B2 |
A1 | 0.017 | |||||
A2a | 0.076 | 0.013 | ||||
A2b1 | 0.077 | 0.043 | 0.016 | |||
A2b2 | 0.079 | 0.047 | 0.036 | 0.011 | ||
B1 | 0.225 | 0.225 | 0.226 | 0.224 | 0.018 | |
B2 | 0.226 | 0.225 | 0.227 | 0.225 | 0.073 | 0.017 |
Subtypes | tMRCAs of Each Viral Gene | |||||||
---|---|---|---|---|---|---|---|---|
N | P | M | F | M2 | SH | G | L | |
All | 1827 | 1775 | 1812 | 1844 | 1859 | 1645 | 1761 | 1754 |
A | 1938 | 1937 | 1943 | 1948 | 1950 | 1937 | 1937 | 1925 |
A1 | 1978 | 1972 | 1979 | 1975 | 1979 | 1972 | 1970 | 1973 |
A2 | 1977 | 1978 | 1980 | 1982 | 1985 | 1971 | 1980 | 1977 |
A2a | 1994 | 1993 | 1993 | 1994 | 1994 | 1989 | 1993 | 1992 |
A2b | 1992 | 1991 | 1992 | 1993 | 1996 | 1980 | 1991 | 1989 |
A2b1 | 1994 | 1994 | 1996 | 1997 | 1998 | 1991 | 1996 | 1995 |
A2b2 | 2003 | 2003 | 2004 | 2005 | 2005 | 2004 | 2002 | 2002 |
B | 1945 | 1924 | 1940 | 1948 | 1948 | 1934 | 1939 | 1933 |
B1 | 1979 | 1984 | 1979 | 1975 | 1982 | 1969 | 1978 | 1980 |
B2 | 1978 | 1950 | 1972 | 1978 | 1975 | 1969 | 1972 | 1969 |
- | The Current Study | Regev et al. | Nidaira et al. |
---|---|---|---|
Reference | - | [23] | [22] |
The number of viruses analyzed | 161 strains | 26 strains | 41 strains |
Analyzed region | Full genome sequences (13 kb) | Partial F gene sequences (111 b) | Partial F gene sequences (321 b) |
Phylogenetic analysis | Maximum likelihood analysis (IQ-TREE 2) | Nearest neighbor joint analysis (Clustal X) | Neighbor-joining analysis (MEGA) |
Molecular clock phylogenies | Bayesian MCMC approach (BEAST2) | ND * | ND |
Classification of HMPV A2 strains | A2a, A2b1, and A2b2 | A2a, A2b1, and A2b2 | A2a, A2b, and A2c |
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Nao, N.; Saikusa, M.; Sato, K.; Sekizuka, T.; Usuku, S.; Tanaka, N.; Nishimura, H.; Takeda, M. Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains. Microorganisms 2020, 8, 1280. https://doi.org/10.3390/microorganisms8091280
Nao N, Saikusa M, Sato K, Sekizuka T, Usuku S, Tanaka N, Nishimura H, Takeda M. Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains. Microorganisms. 2020; 8(9):1280. https://doi.org/10.3390/microorganisms8091280
Chicago/Turabian StyleNao, Naganori, Miwako Saikusa, Ko Sato, Tsuyoshi Sekizuka, Shuzo Usuku, Nobuko Tanaka, Hidekazu Nishimura, and Makoto Takeda. 2020. "Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains" Microorganisms 8, no. 9: 1280. https://doi.org/10.3390/microorganisms8091280