不過似乎從搜尋工具沒辦法直接做到這點, 所以就從 wuhan 開始吧.
https://www.ncbi.nlm.nih.gov/nuccore/?term=wuhan
選擇用 Viruses 過濾, 從 3. 4. 看到重點了.
3.
29,903 bp linear RNA
4.
29,903 bp linear RNA
- Accession:
- NC_045512.2
- GI:
- 1798174254
這不就是熱騰騰的全基因體序列, 得來全不費功夫.
重點這是海鮮市場的, 就是這場瘟疫的重點之一.
至於起點, 直到今日(01/28)還全無頭緒.
接下來就用 3. 4. 進行 BLASTN https://blast.ncbi.nlm.nih.gov/Blast.cgi
請輸入 MN908947.3 |NC_045512.2 (分兩行), 使用 Highly similar sequences (megablast)
因為病毒基因體只有 29.9kb 左右, 所以迅速找到相似的序列.
Select for downloading or viewing reports | Description | Max Score | Total Score | Query Cover | E value | Per. Ident | Accession |
---|---|---|---|---|---|---|---|
26943 | 35336 | 95% | 0.0 | 89.12% | |||
22223 | 35276 | 94% | 0.0 | 88.65% | |||
15213 | 22564 | 88% | 0.0 | 82.34% | |||
15213 | 22600 | 88% | 0.0 | 82.34% | |||
15202 | 22531 | 88% | 0.0 | 82.33% | |||
15202 | 22529 | 88% | 0.0 | 82.33% | |||
15191 | 22548 | 88% | 0.0 | 82.32% | |||
15186 | 22483 | 88% | 0.0 | 82.32% | |||
15186 | 22276 | 87% | 0.0 | 82.31% | |||
15186 | 22577 | 88% | 0.0 | 82.32% | |||
15180 | 22548 | 88% | 0.0 | 82.31% | |||
15180 | 22507 | 88% | 0.0 | 82.31% | |||
15180 | 22566 | 88% | 0.0 | 82.31% | |||
15180 | 22526 | 88% | 0.0 | 82.31% | |||
15176 | 22618 | 91% | 0.0 | 82.32% | |||
15176 | 22534 | 91% | 0.0 | 82.30% | |||
15175 | 22417 | 88% | 0.0 | 82.30% | |||
15175 | 22424 | 88% | 0.0 | 82.30% | |||
15175 | 22417 | 88% | 0.0 | 82.30% | |||
15175 | 22529 | 88% | 0.0 | 82.30% | |||
15175 | 22450 | 88% | 0.0 | 82.30% | |||
15175 | 22574 | 88% | 0.0 | 82.30% | |||
15175 | 22579 | 88% | 0.0 | 82.30% | |||
15175 | 22529 | 88% | 0.0 | 82.30% | |||
15175 | 22516 | 88% | 0.0 | 82.30% | |||
15175 | 22504 | 88% | 0.0 | 82.30% | |||
15175 | 22502 | 88% | 0.0 | 82.30% | |||
15175 | 22504 | 88% | 0.0 | 82.30% | |||
15175 | 22526 | 88% | 0.0 | 82.30% | |||
15175 | 22513 | 88% | 0.0 | 82.30% | |||
15175 | 22502 | 88% | 0.0 | 82.30% | |||
15175 | 22568 | 88% | 0.0 | 82.30% | |||
15175 | 22579 | 88% | 0.0 | 82.30% | |||
15175 | 22539 | 88% | 0.0 | 82.30% | |||
15175 | 22533 | 88% | 0.0 | 82.30% | |||
15175 | 22526 | 88% | 0.0 | 82.30% | |||
15175 | 22539 | 88% | 0.0 | 82.30% | |||
15175 | 22511 | 88% | 0.0 | 82.30% | |||
15175 | 22561 | 88% | 0.0 | 82.30% | |||
15175 | 22555 | 88% | 0.0 | 82.30% | |||
15175 | 22561 | 88% | 0.0 | 82.31% | |||
15175 | 22566 | 88% | 0.0 | 82.31% | |||
15175 | 22566 | 88% | 0.0 | 82.30% | |||
15175 | 22548 | 88% | 0.0 | 82.30% | |||
15175 | 22535 | 88% | 0.0 | 82.30% | |||
15175 | 22461 | 88% | 0.0 | 82.30% | |||
15175 | 22563 | 88% | 0.0 | 82.30% | |||
15175 | 22561 | 88% | 0.0 | 82.30% | |||
15175 | 22522 | 88% | 0.0 | 82.30% | |||
15175 | 22528 | 88% | 0.0 | 82.30% | |||
15175 | 22535 | 88% | 0.0 | 82.30% | |||
15173 | 22415 | 88% | 0.0 | 82.30% | |||
15171 | 22424 | 88% | 0.0 | 82.30% | |||
15169 | 22420 | 88% | 0.0 | 82.30% | |||
15169 | 22415 | 88% | 0.0 | 82.30% | |||
15169 | 22504 | 88% | 0.0 | 82.30% | |||
15169 | 22509 | 88% | 0.0 | 82.30% | |||
15169 | 22509 | 88% | 0.0 | 82.30% | |||
15169 | 22574 | 88% | 0.0 | 82.30% | |||
15169 | 22535 | 88% | 0.0 | 82.30% | |||
15169 | 22518 | 88% | 0.0 | 82.29% | |||
15169 | 22561 | 88% | 0.0 | 82.30% | |||
15169 | 22546 | 88% | 0.0 | 82.30% | |||
15167 | 22526 | 88% | 0.0 | 82.29% | |||
15165 | 22406 | 88% | 0.0 | 82.29% | |||
15163 | 21673 | 85% | 0.0 | 82.29% | |||
15158 | 22498 | 88% | 0.0 | 82.29% | |||
15149 | 22403 | 88% | 0.0 | 82.29% | |||
15134 | 22372 | 86% | 0.0 | 82.26% | |||
15117 | 22368 | 88% | 0.0 | 82.26% | |||
15084 | 16332 | 64% | 0.0 | 82.35% | |||
15043 | 21834 | 86% | 0.0 | 82.18% | |||
14970 | 22339 | 87% | 0.0 | 82.20% | |||
14916 | 22163 | 87% | 0.0 | 82.16% | |||
14892 | 21819 | 88% | 0.0 | 82.00% | |||
14759 | 23767 | 91% | 0.0 | 81.89% | |||
14731 | 21836 | 87% | 0.0 | 82.02% | |||
14722 | 21360 | 87% | 0.0 | 81.82% | |||
14683 | 21261 | 86% | 0.0 | 81.79% | |||
14683 | 21067 | 86% | 0.0 | 81.79% | |||
14683 | 21958 | 88% | 0.0 | 81.82% | |||
14678 | 21996 | 88% | 0.0 | 81.82% | |||
14628 | 21416 | 87% | 0.0 | 81.74% | |||
14556 | 21386 | 87% | 0.0 | 81.66% | |||
14556 | 21394 | 87% | 0.0 | 81.66% | |||
14550 | 21830 | 88% | 0.0 | 81.68% | |||
14539 | 15829 | 66% | 0.0 | 81.66% | |||
14517 | 21878 | 89% | 0.0 | 81.65% | |||
14512 | 21810 | 88% | 0.0 | 81.64% | |||
14506 | 21791 | 88% | 0.0 | 81.63% | |||
14506 | 21797 | 88% | 0.0 | 81.63% | |||
14501 | 21780 | 88% | 0.0 | 81.63% | |||
14501 | 21863 | 89% | 0.0 | 81.63% | |||
14501 | 21849 | 89% | 0.0 | 81.63% | |||
14495 | 21769 | 88% | 0.0 | 81.63% | |||
14495 | 21797 | 88% | 0.0 | 81.62% | |||
14484 | 21758 | 88% | 0.0 | 81.61% | |||
14484 | 21758 | 88% | 0.0 | 81.61% | |||
13501 | 20280 | 79% | 0.0 | 82.94% | |||
13452 | 20206 | 79% | 0.0 | 82.88% |
使用圖形化顯示
發現武漢海鮮市場樣本大致上包含第一與第二筆, 但是有一段卻多出來了.
那一段大概在 22000 ~ 23400 約 1400 bps.
此時調出武漢海鮮市場樣本 01/23 的較新版全基因體
https://www.ncbi.nlm.nih.gov/nuccore/MN908947.3
找出 22000 ~ 23400 序列.
aaaaacaacaaaagttggatggaaagtgagttcagagtttattctagtgcgaataattgcacttttgaatatgtctctcagccttttcttatggaccttgaaggaaaacagggtaatttcaaaaatcttagggaatttgtgtttaagaatattgatggttattttaaaatatattctaagcacacgcctattaatttagtgcgtgatctccctcagggtttttcggctttagaaccattggtagatttgccaataggtattaacatcactaggtttcaaactttacttgctttacatagaagttatttgactcctggtgattcttcttcaggttggacagctggtgctgcagcttattatgtgggttatcttcaacctaggacttttctattaaaatataatgaaaatggaaccattacagatgctgtagactgtgcacttgaccctctctcagaaacaaagtgtacgttgaaatccttcactgtagaaaaaggaatctatcaaacttctaactttagagtccaaccaacagaatctattgttagatttcctaatattacaaacttgtgcccttttggtgaagtttttaacgccaccagatttgcatctgtttatgcttggaacaggaagagaatcagcaactgtgttgctgattattctgtcctatataattccgcatcattttccacttttaagtgttatggagtgtctcctactaaattaaatgatctctgctttactaatgtctatgcagattcatttgtaattagaggtgatgaagtcagacaaatcgctccagggcaaactggaaagattgctgattataattataaattaccagatgattttacaggctgcgttatagcttggaattctaacaatcttgattctaaggttggtggtaattataattacctgtatagattgtttaggaagtctaatctcaaaccttttgagagagatatttcaactgaaatctatcaggccggtagcacaccttgtaatggtgttgaaggttttaattgttactttcctttacaatcatatggtttccaacccactaatggtgttggttaccaaccatacagagtagtagtactttcttttgaacttctacatgcaccagcaactgtttgtggacctaaaaagtctactaatttggttaaaaacaaatgtgtcaatttcaacttcaatggtttaacaggcacaggtgttcttactgagtctaacaaaaagtttctgcctttccaacaatttggcagagacattgctgacactactgatgctgtccgtgatccacagacacttgagattcttgacattacaccatgttcttttggtggtgtcagtgttataacaccaggaacaaatacttctaaccaggttgctgttctttatca
再到 BLASTN 用這段序列進行搜尋, 這次找到不多序列. 但是有趣的結果來了.
- 其中 500 ~ 850 左右的片段與右方的序列群不同只找到一筆資料, 卻更增加想像空間.
- 這是從日本野生蝙蝠取得的冠狀病毒 Spkie 蛋白 S 基因的序列.
-
LOCUS LC469301 558 bp RNA linear VRL 21-SEP-2019 DEFINITION Bat coronavirus Rc-CoV-3 S gene for Spike protein, partial cds. ACCESSION LC469301 VERSION LC469301.1 KEYWORDS . SOURCE Bat coronavirus ORGANISM Bat coronavirus Viruses; Riboviria; Nidovirales; Cornidovirineae; Coronaviridae; Coronavirinae; unclassified coronaviruses. REFERENCE 1 AUTHORS Kobayashi,T., Murakami,S. and Horimoto,T. TITLE Novel coronaviruses harbored by wild bats in Japan JOURNAL Unpublished REFERENCE 2 (bases 1 to 558) AUTHORS Kobayashi,T., Murakami,S. and Horimoto,T. TITLE Direct Submission JOURNAL Submitted (20-MAR-2019) Contact:Tomoya Kobayashi The Universtiy of Tokyo, Department of veterinary microbiology; 1-1-1 Yayoi Bunkyo-ku, Tokyo, Tokyo 113-8657, Japan FEATURES Location/Qualifiers source 1..558 /organism="Bat coronavirus" /mol_type="genomic RNA" /strain="Rc-CoV-3" /host="Rhinolophus cornutus" /db_xref="taxon:1508220" /country="Japan"
https://www.ncbi.nlm.nih.gov/nucleotide/LC469301.1?report=genbank&log$=nucltop&blast_rank=5&RID=2VJ0F2KE014
可能原因有:
1. 此區塊與致病相關, 所以有較大數量的定序成品.
2. 左方的區塊可能被認為與致病不相關?
3. 左方區塊出現僅在此次捕捉的野生蝙蝠樣本出現, 就未曾出現.
只是比較多數蝙蝠基因體序列和武漢海鮮市場樣本,
發現武漢海鮮市場樣本多了 22000 ~ 23400 這一段完整的序列.
排除此段為定序難度高區域. 但是武漢的樣本多了這麼一段,
是大自然演化的結果或是人為操控剪接基因造成的???
讓我們繼續看下去.
現在首重在找出病源, 讓檢驗方法簡易且快速. 畢竟潛伏期就能傳染實在
讓發燒篩檢的成果打了折扣. 更重要的是要在最短時間生產出解方及疫苗.
要不然已經發病的患者不能等很久的.
參考資料:
1. NCBI https://www.ncbi.nlm.nih.gov/
https://blast.ncbi.nlm.nih.gov/Blast.cgi
2. 各種動物與人類冠狀病毒之比較 https://www.coa.gov.tw/ws.php?id=5092