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研究生:陳小飛
研究生(外文):Cindy Geniola
論文名稱:臺灣蝙蝠冠狀病毒的調查及序列分析
論文名稱(外文):Detection of bat coronavirus in the bat population of Taiwan
指導教授:陳怡寧陳怡寧引用關係
指導教授(外文):Chen Yi-Ning
學位類別:碩士
校院名稱:中原大學
系所名稱:生物科技研究所
學門:生命科學學門
學類:生物科技學類
論文種類:學術論文
論文出版年:2019
畢業學年度:107
語文別:英文
論文頁數:106
中文關鍵詞:蝙蝠冠狀病毒RdRp檢測台灣
外文關鍵詞:Bats coronavirusRdRp detectionTaiwan
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已知蝙蝠是幾種病毒的天然宿主,例如埃博拉病毒(EBOV),嚴重急性呼吸綜合症冠狀病毒(SARS-CoV)和中東呼吸綜合徵冠狀病毒(MERS-CoV)。我們從2013 - 2018年收集了總共872個蝙蝠糞便樣本,其中包括24種蝙蝠物種,並確定了性別,年齡和繁殖狀況,以供進一步分析。本研究中台灣CoV的總患病率為20%,共有177個陽性樣本。 Scotophilus kuhlii,Miniopterus fuliginosus和Rhinolophus monoceros的樣本量最大,CoV流行率分別為43%(76/178),22%(27/123)和17%(43/247)。成年蝙蝠,亞成體蝙蝠,雄性蝙蝠和雌性蝙蝠的冠狀病毒流行率分別為26%(131/499),26%(35/135),21%(79/373)和21%(91/428) 。年齡,性別和女性生育狀況不影響所有蝙蝠物種的CoV流行率。然而,交配雄性蝙蝠(34%,19/56)的CoV流行率顯著高於準備交配的雄性蝙蝠(17%,10/60)和非交配雄性蝙蝠(21%,5/39)。在本研究中,從Eptesicus serotinus horikawai中分離出Betacoronavirus c(E5-4和E10-1與中國蝙蝠中檢測到的MERS相關CoV具有高核苷酸同一性。我們的Betacoronavirus c菌株(E5-4和E10-1)之間的核苷酸同一性並且BatCoV-NL140422-China-2014分離株為97.9%,所有三株分離株在系統發育樹中聚集在一起。在S. kuhlii,M.fuliginosus和R. monoceros中檢測到的α冠狀病毒序列均高度相似。 Scotophilus bat CoV-512。經過6年的監測,我們在台灣蝙蝠種群中觀察到了α和β病毒的地方性流行,這些信息可以作為參考,為未來的冠狀病毒爆發做準備。
Bats are known to be the natural reservoir of several viruses, such as Ebola virus (EBOV), severe acute respiratory syndrome coronavirus (SARS-CoV), and Middle East respiratory syndrome coronavirus (MERS-CoV). We collected a total of 872 bat fecal samples of 24 bats species from 2013-2018 and identified the gender, age, and reproductive status for further analysis. The total prevalence of CoV in Taiwan in this study was 20% with a total of 177 positive samples. Scotophilus kuhlii, Miniopterus fuliginosus, and Rhinolophus monoceros had the largest sample size and high CoV prevalence of 43% (76/178), 22% (27/123), and 17% (43/247), respectively. The CoV prevalence of adult bats, subadult bats, male bats, and female bats were 26% (131/499), 26% (35/135), 21% (79/373) and 21% (91/428), respectively. Age, gender, and female reproductive status did not influence the CoV prevalence of all bat species. However, the mating male bats (34%, 19/56) had significant higher CoV prevalence than male bats prepare-to-mate (17%, 10/60) and non-mating male bats (21%, 5/39). Betacoronavirus c isolated from Eptesicus serotinus horikawai in this study (E5-4 and E10-1 had high nucleotide identity with MERS-related CoV detected in the bats in China. The nucleotide identity between our Betacoronavirus c isolates (E5-4 and E10-1) and BatCoV-NL140422-China-2014 isolate was 97.9% and all three isolates were clustered together in the phylogenetic tree. Sequences of the alphacoronavirus detected in S. kuhlii, M. fuliginosus, and R. monoceros were all highly similar to those of Scotophilus bat CoV-512. After 6 years of surveillance, we observed the endemic circulation of alpha- and betacoronavirus in the bat population of Taiwan and the information can be used as references to prepare for a future outbreak of CoV.
Contents

摘要 i
Abstract ii
Acknowledgement iii
Contents iv
List of Tables vi
List of Figures vii
1. Introduction 1
2. Motivation and Object 2
3. Literature Review 3
3.1 Bats as Pathogens Natural Reservoir 3
3.2 Roles of Bats in Diseases 4
3.3 Coronavirus-related Disease and Transmission 5
3.4 Coronavirus Characteristics 7
3.5 Coronavirus Viral Infection Mechanism 9
3.6 RNA-dependent RNA Polymerase Gene 10
3.7 Severe Acute Respiratory Syndrome Coronavirus 12
3.8 Middle East Respiratory Syndrome Coronavirus 14
3.9 Scotophilus Bat Coronavirus 16
4. Research Design and Materials 18
4.1 Experimental Design 18
4.2 Fecal Sampling 18
4.3 RNA Extraction and Reverse Transcription 19
4.4 PCR Amplification and Sequencing 20
4.5 PCR Amplicon Ligation 21
4.6 Transformation 21
4.7 Plasmid Extraction and Purification 22
4.8 Phylogenetic Analysis 22
4.9 Statistical Analysis 23
5. Result 24
5.1 Bat Coronavirus Prevalence in Taiwan from 2013 to 2018 24
5.2 Correlation Between Gender, Age and Reproductive Status 24
5.3 Major Bats Coronavirus Prevalence in Taiwan from 2013 to 2018 25
5.4 Major Bats Coronavirus Prevalence Correlation Between Gender, Age and Reproductive Status. 26
5.5 Major Bats Coronavirus Prevalence in Taiwan in 2018 27
5.6 Phylogenetic Analysis of Bat Coronavirus Detected in Taiwan 27
6. Discussion 32
7. Conclusion 39
APPENDIX 79
REFERENCES 71

List of Tables

Table 1. Host species of Coronaviridae family 40
Table 2. SARS coronavirus infection in several susceptible animal species
(Wang et al., 2006) 41
Table 3. Coronavirus in bats detected in China and Hong Kong
(Wang et al., 2006) 42
Table 4. Samples information from 24 bats species in Taiwan from 2013 to 2018 44
Table 5. Coronavirus Gender, Age and Reproductive Status prevalence in Taiwan
from 2013 to 2018 45
Table 6. Major Bats prevalence in Taiwan from 2013 to 2018 45
Table 7. Major Bats Gender, Age, and Reproductive Status Prevalence in Taiwan
from 2013 to 2018 46
Table 8. Major Bats Gender and Age Prevalence Comparison in Taiwan
from 2013 to 2018 46
Table 9. List of coronavirus RNA-dependent RNA polymerase gene sequences from GenBank for phylogenetic tree analysis 50
Table 10. Phylogenetic tree sample list 51
Table 11. Partial RNA-dependent RNA polymerase nucleotide sequences of isolated bat coronavirus 54


List of Figures

Figure 1. Phylogenetic tree based on partial RNA-dependent RNA polymerase gene (440bp) fragment of three bat CoVs detected in Taiwan (Chen et al., 2016) 54
Figure 2. SARS-CoV morphology in microscope electron and structure composition of SARS-CoV (Stadler et al., 2003) 55
Figure 3. Coronavirus genome structure different group comparison (Stadler et al., 2003) 55
Figure 4. Coronavirus viral infection mechanism (Masters, 2006; Fehr and Perlman, 2015) 56
Figure 5. Phylogenetic relationships comparison of the helicase (A) and spike (B) genes of coronaviruses isolated from bats in China (Tang et al., 2006) 56
Figure 6. SARS-CoV immune evasion mechanism (de Wit et al., 2016) 57
Figure 7. The procedure for the genomic characterization of bat coronavirus 57
Figure 8. Gel electrophoresis result for coronavirus RNA-dependent RNA polymerase gene detection 57
Figure 9. Gel electrophoresis result for coronavirus RNA-dependent RNA polymerase gene detection with smear result example 58
Figure 10. Bat coronavirus distribution in Taiwan from 2013 to 2018 58
Figure 11. Scotophilus kuhlii coronavirus detection rate in Taiwan in 2018 59
Figure 12. Rhinolophus monoceros coronavirus detection rate in Taiwan in 2018 60
Figure 13. Phylogenetic tree based on partial RNA-dependent RNA polymerase gene fragment of 44 coronaviruses isolated from bats in Taiwan from 2013 to 2018 61
Figure 14. Phylogenetic tree based on partial RNA-dependent RNA polymerase gene fragment of Alphacoronavirus CoV sample 62
Figure 15. Phylogenetic tree based on partial RNA-dependent RNA polymerase gene fragment of Betacoronavirus CoV sample 63
Figure 16. Phylogenetic tree based on partial RNA-dependent RNA polymerase gene fragment of Scotophilus 512 related CoV and PEDV 64
Figure 17. Phylogenetic tree based on partial RNA-dependent RNA polymerase gene fragment of Miniopterus related CoV sample 65
Figure 18. Phylogenetic tree based on partial RNA-dependent RNA polymerase gene fragment of SARS-related CoV sample 66
Figure 19. Phylogenetic tree based on partial RNA-dependent RNA polymerase gene fragment of MERS-related CoV sample 67
Figure 20. Phylogenetic tree nucleotide substitution models Kimura and GTR+Gamma+I comparison on phylogenetic tree based on partial RNA-dependent RNA polymerase gene fragment of Miniopterus-related CoV samples 68
Figure 21. Phylogenetic tree nucleotide substitution models Kimura and GTR+Gamma+I comparison on phylogenetic tree based on partial RNA-dependent RNA polymerase gene fragment of SARS-related CoV samples 68
Figure 22. Phylogenetic tree nucleotide substitution models Kimura and GTR+Gamma+I comparison on phylogenetic tree based on partial RNA-dependent RNA polymerase gene fragment of SARS-related CoV samples with highlight on bat SARS-related CoV group 69
Figure 23. Phylogenetic tree nucleotide substitution models Kimura and GTR+Gamma+I comparison on phylogenetic tree based on partial RNA-dependent RNA polymerase gene fragment of Betacoronavirus lineage 2c related samples 69
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