Identification of a Novel Betacoronavirus (Merbecovirus) in Amur Hedgehogs from China
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Sample Collection
2.3. Detection of CoVs by RT-PCR and Sequencing
2.4. Viral Culture
2.5. Complete Genome Sequencing and Analysis of Ea-HedCoV HKU31
2.6. Estimation of Divergence Dates
2.7. Structural Modelling of Ea-HedCoV HKU31 Receptor-Binding Domain (RBD)
2.8. Recombination Analysis
2.9. Nucleotide Sequence Accession Numbers
3. Results
3.1. Detection of CoVs in Animals and Discovery of a Novel Species of Merbecovirus from Amur Hedgehogs
3.2. Genome Organization of Ea-HedCoV HKU31
3.3. Sequence Analysis and Structural Modelling of the Ea-HedCoV HKU31 Spike Protein
3.4. Phylogenetic Analysis
3.5. Estimation of Divergence Dates
3.6. Recombination Analysis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
BetaCoV | Betacoronavirus |
bp | Base pair |
CoVs | Coronaviruses |
HCoV | Human coronavirus |
MERS-CoV | Middle East respiratory syndrome coronavirus |
ORF | Open reading frame |
PCR | Polymerase chain reaction |
Pi | Pipistrellus |
RdRp | RNA-dependent RNA polymerase |
RT | Reverse transcription |
S | Spike |
SARSr-CoV | Severe Acute Respiratory Syndrome-related coronavirus |
TRS | Transcription regulatory sequence |
Ty | Tylonycteris |
µL | Microliter |
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Genome Features | Pairwise aa Sequence Identity with Ea-HedCoV HKU31 Strain F6 Sequence (%) | ||||||||
---|---|---|---|---|---|---|---|---|---|
Coronavirus | Size (No. of Bases) | G+C Content | 3CLPro | RdRp | Hel | S | E | M | N |
Merbecovirus | |||||||||
Hp-BatCoV HKU25 | 30,497 | 0.42 | 79.4 | 90.0 | 92.5 | 57.1 | 76.8 | 78.4 | 67.2 |
BtVs-BetaCoV/SC2013 | 30,423 | 0.43 | 78.4 | 90.7 | 92.6 | 57.3 | 79.3 | 79.8 | 68.9 |
Human MERS-CoV ChinaGD01 | 30,114 | 0.41 | 77.8 | 89.4 | 91.3 | 57.5 | 73.2 | 79 | 66.7 |
Human MERS-CoV England1 | 30,111 | 0.41 | 77.8 | 89.3 | 91.3 | 57.7 | 73.2 | 78.5 | 67.2 |
Human MERS-CoV EMC/2012 | 30,119 | 0.41 | 77.8 | 89.4 | 91.1 | 57.7 | 73.2 | 79 | 67.2 |
Camel MERS-CoV NRCE-HKU205 | 29,908 | 0.41 | 78.1 | 89.4 | 91.1 | 57.8 | 73.2 | 79 | 66.4 |
Camel MERS-CoV Jeddah-1 | 29,851 | 0.41 | 77.8 | 89.4 | 91.3 | 57.7 | 73.2 | 79 | 67.2 |
NeoCoV | 30,111 | 0.40 | 77.1 | 89.2 | 91.6 | 63.4 | 75.6 | 80.4 | 69.7 |
Ty-BatCoV HKU4 | 30,286 | 0.38 | 71.2 | 87.6 | 90.8 | 57.5 | 64.6 | 77.6 | 63.8 |
Pi-BatCoV HKU5 | 30,488 | 0.43 | 75.5 | 89.1 | 91 | 57.7 | 62.2 | 79.1 | 63.8 |
BetaCoV/Erinaceus/VMC/DEU | 30,175 | 0.37 | 85.6 | 92.2 | 96.2 | 77.9 | 84.1 | 90.8 | 84.8 |
Ea-HedCoV HKU31 RS13 | 29,951 | 0.38 | 100 | 100 | 100 | 99.9 | 100 | 100 | 96.5 |
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Lau, S.K.P.; Luk, H.K.H.; Wong, A.C.P.; Fan, R.Y.Y.; Lam, C.S.F.; Li, K.S.M.; Ahmed, S.S.; Chow, F.W.N.; Cai, J.-P.; Zhu, X.; et al. Identification of a Novel Betacoronavirus (Merbecovirus) in Amur Hedgehogs from China. Viruses 2019, 11, 980. https://doi.org/10.3390/v11110980
Lau SKP, Luk HKH, Wong ACP, Fan RYY, Lam CSF, Li KSM, Ahmed SS, Chow FWN, Cai J-P, Zhu X, et al. Identification of a Novel Betacoronavirus (Merbecovirus) in Amur Hedgehogs from China. Viruses. 2019; 11(11):980. https://doi.org/10.3390/v11110980
Chicago/Turabian StyleLau, Susanna K. P., Hayes K. H. Luk, Antonio C. P. Wong, Rachel Y. Y. Fan, Carol S. F. Lam, Kenneth S. M. Li, Syed Shakeel Ahmed, Franklin W.N. Chow, Jian-Piao Cai, Xun Zhu, and et al. 2019. "Identification of a Novel Betacoronavirus (Merbecovirus) in Amur Hedgehogs from China" Viruses 11, no. 11: 980. https://doi.org/10.3390/v11110980