Discussion: Comparing 2 GenBank coronavirus submittals QHD43418.1 and AVP78033.1 - 100% genome match for 78 sequences on the envelope protein? 2019-n

[sharon sanders]

I copied this post from another thread we have on the site. This is the research paper related to AVP78033.1. We have been looking at this interesting study.



The China scientific community has the genetic material. In this 2018 study they used mammals, and proposed further such studies.

Key word: infectivity


Emerg Microbes Infect. 2018; 7: 154.
Published online 2018 Sep 12. doi: 10.1038/s41426-018-0155-5
PMCID: PMC6135831
PMID: 30209269


Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats


Dan Hu,[SUP]1,[/SUP][SUP]2[/SUP]Changqiang Zhu,[SUP]2[/SUP]Lele Ai,[SUP]2[/SUP]Ting He,[SUP]2[/SUP]Yi Wang,[SUP]3[/SUP]Fuqiang Ye,[SUP]2[/SUP]Lu Yang,[SUP]2[/SUP]Chenxi Ding,[SUP]2[/SUP]Xuhui Zhu,[SUP]2[/SUP]Ruicheng Lv,[SUP]2[/SUP]Jin Zhu,[SUP]2[/SUP]Bachar Hassan,[SUP]4[/SUP]Youjun Feng,[SUP]

[/SUP][SUP]5[/SUP]Weilong Tan,[SUP]

[/SUP][SUP]2[/SUP] and Changjun Wang[SUP]

[/SUP][SUP]1,[/SUP][SUP]2[/SUP]
Author information Article notes Copyright and License information Disclaimer
[SUP]1[/SUP]Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038 China
[SUP]2[/SUP]Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002 China
[SUP]3[/SUP]Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province 214064 P.R. China
[SUP]4[/SUP]Stony Brook University, Stony Brook, 11794 USA
[SUP]5[/SUP]Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
Youjun Feng, Email: nc.ude.ujz@jygnef.
Contributor Information.
[SUP]

[/SUP]Corresponding author.
This article has been cited by other articles in PMC.

Associated Data

Supplementary Materials
Go to: Abstract


SARS coronavirus (SARS-CoV), the causative agent of the large SARS outbreak in 2003, originated in bats. Many SARS-like coronaviruses (SL-CoVs) have been detected in bats, particularly those that reside in China, Europe, and Africa. To further understand the evolutionary relationship between SARS-CoV and its reservoirs, 334 bats were collected from Zhoushan city, Zhejiang province, China, between 2015 and 2017. PCR amplification of the conserved coronaviral protein RdRp detected coronaviruses in 26.65% of bats belonging to this region, and this number was influenced by seasonal changes. Full genomic analyses of the two new SL-CoVs from Zhoushan (ZXC21 and ZC45) showed that their genomes were 29,732 nucleotides (nt) and 29,802 nt in length, respectively, with 13 open reading frames (ORFs). These results revealed 81% shared nucleotide identity with human/civet SARS CoVs, which was more distant than that observed previously for bat SL-CoVs in China. Importantly, using pathogenic tests, we found that the virus can reproduce and cause disease in suckling rats, and further studies showed that the virus-like particles can be observed in the brains of suckling rats by electron microscopy. Thus, this study increased our understanding of the genetic diversity of the SL-CoVs carried by bats and also provided a new perspective to study the possibility of cross-species transmission of SL-CoVs using suckling rats as an animal model.


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135831/

 

[sharon sanders]

from a friend of FluTrackers -

GenBank version QHD43418.1 is the submittal number from the envelope protein from the current 2019-nCov entered January 17, 2020.

GenBank version AVP78033.1 is the submittal number from the envelope protein for Bat SARS-like coronavirus January 5, 2018


"Using the BLAST tool from US National Library of Medicine, running multigenetic genome matches on these two genetic sequences, for 78 sequences, a 100% match on the envelope protein occurs."

 

[sharon sanders]

bump this

 

[gsgs]

ZXC21 and ZC45 were the 2 closest to nCoV , until we saw RaTG13, which is much closer.
The envelope Protein is pretty short, is a match common in coronaviruses ? I'll check ,
but wouldn't be surprised. But how many nucleotide-differences ?
MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVS LVKPSFYVYSRVKNLNSSRVPDLLV
mysfvseetg tlivnsvllf lafvvfllvt lailtalrlc ayccnivnvs lvkpsfyvys rvknlnssrv pdllv

================================================== ============


Wuhan virus:
https://www.ncbi.nlm.nih.gov/nuccore/MN908947


gene 26245..26472
/gene="E"
CDS 26245..26472
/gene="E"
/note="structural protein; E protein"
/codon_start=1
/product="envelope protein"
/protein_id="QHD43418.1"
/translation="MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTAL RLCAYCC
NIVNVSLVKPSFYVYSRVKNLNSSRVPDLLV"


================================================== ===============

https://www.ncbi.nlm.nih.gov/protein/AVP78033
/organism="Bat SARS-like coronavirus" /isolate="bat-SL-CoVZC45" /host="Rhinolophus sinicus" /db_xref="taxon:1508227" /country="China" /collection_date="Feb-2017" Protein 1..75 /product="envelope protein" /name="E" CDS 1..75 /coded_by="MG772933.1:26150..26377" ORIGIN 1 mysfvseetg tlivnsvllf lafvvfllvt lailtalrlc ayccnivnvs lvkpsfyvys 61 rvknlnssrv pdllv //

ZXC45 :

================================================== ============================

same nucleotides in the envelope area for ZXC21 and ZC45 and 3 nucleotide-differences to Wuhan-hu-1,
which makes 98.7% identity in that area

[FONT=Arial]>ZXC21 , 26081..26308
ATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTTGTGGTATTCTTGCTAGTCACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTTTGGTCTAA
>ZC45  , 26150..26377
ATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTTGTGGTATTCTTGCTAGTCACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTTTGGTCTAA
>Wuhan-Hu-1  ,  26245..26472
ATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAA[/FONT]

===============================================================

for the envelope protein these 3 viruses are clearly separated from the others at genbank
and they are much more similar than in total (recombination ?)

                                                                                                                 000000000000000000000000000000000000000000000000000000000000000
                                                                                                                 000000000000000000000000011111111111111111111111222222222222222
                                                                                                                 011112245556667777888999912234555666667778899999000000011112222
                                                                                                                 523895813681240159389012714645247345672351723489234678901260149
-codon-position--------------------------------------------------------------------------------------------------2 1 111222112112 1212 121 1 2121112 1212111 12 112 2 12 12 1221
---Index---------------------------------------------------------------------------------------------------------ACGCGAAGCCTTCTCGTCCCACACCTGAACTAAAACGGCGCGTATCACTTCGAAGGAGCTCCC
   1 >JX993987.1 Bat coronavirus Rp/Shaanxi2011, complete genome                                                 ...........CT.......................A...TA..........T..........
   2 >KF294457.1 SARS-related bat coronavirus isolate Longquan-140 ,   complete cds                              .....G.....CT.......................A...TA...........G.........
   3 >DQ084199.1 bat SARS coronavirus HKU3-2, complete genome                                                    .....G.....C........................A...TA...........G.........
   4 >GQ153540.1 Bat SARS coronavirus HKU3-5, complete genome                                                    .....G.....C........................A...TA...........G.........
   5 >DQ022305.2 Bat SARS coronavirus HKU3-1, complete genome                                                    .....G.....C........................A...TA...........G.........
   6 >GQ153547.1 Bat SARS coronavirus HKU3-12, complete genome                                                   .....G.....C........................A...TA...........G.........
   7 >GQ153548.1 Bat SARS coronavirus HKU3-13, complete genome                                                   .....G.....C........................A...TA...........G.........
   8 >GQ153546.1 Bat SARS coronavirus HKU3-11, complete genome                                                   .....G.....C........................A...TA...........G.........
   9 >GQ153539.1 Bat SARS coronavirus HKU3-4, complete genome                                                    .....G.....C........................A...TA...........G.........
  10 >GQ153544.1 Bat SARS coronavirus HKU3-9, complete genome                                                    .....G.....C........................A...TA...........G.........
  11 >GQ153545.1 Bat SARS coronavirus HKU3-10, complete genome                                                   .....G.....C........................A...TA...........G.........
  12 >FJ211859.1 Recombinant coronavirus clone Bat SARS-CoV, complete sequence                                   .....G.....C........................A...TA...........G.........
  13 >GQ153541.1 Bat SARS coronavirus HKU3-6, complete genome                                                    .....G.....C........................A...TA...........G.........
  14 >GQ153543.1 Bat SARS coronavirus HKU3-8, complete genome                                                    .....G..A..C...........A.....T......A...TA...........G.........
  15 >GQ153542.1 Bat SARS coronavirus HKU3-7, complete genome                                                    .....G..A..C.................T......A...TA...........G.........
  16 >DQ084200.1 bat SARS coronavirus HKU3-3, complete genome                                                    .....G.....C........................A...TA...........G.........
  17 >DQ412043.1 Bat SARS coronavirus Rm1, complete genome                                                       ....A.....CCT..................G....A...TA...........G.........
  18 >DQ648857.1 Bat coronavirus (BtCoV/279/2005), complete genome                                               ....A.....C.T.......................A...TA...........G.........
  19 >DQ071615.1 Bat SARS coronavirus Rp3, complete genome                                                       ..........C........T................A...TA.....................
  20 >KF569996.1 Rhinolophus affinis coronavirus isolate LYRa11, complete genome                                 ....................................A...TA....G................
  21 >KJ473814.1 BtRs-BetaCoV/HuB2013, complete genome                                                           .....G......G.......................A...TA.....................
  22 >KJ473816.1 BtRs-BetaCoV/YN2013, complete genome                                                            .....G..............................A...T......................
  23 >KU973692.1 UNVERIFIED: SARS-related coronavirus isolate F46, complete genome                               .....G.....C........................A..........................
  24 >KJ473815.1 BtRs-BetaCoV/GX2013, complete genome                                                            .....G.....C........................A..........................
  25 >JX993988.1 Bat coronavirus Cp/Yunnan2011, complete genome                                                  .....G..................T...........A..........................
  26 >MK211375.1 Coronavirus BtRs-BetaCoV/YN2018A, complete genome                                               ....................................A..........................
  27 >KY417151.1 Bat SARS-like coronavirus isolate Rs7327, complete genome                                       ....................................T..........................
  28 >KY417152.1 Bat SARS-like coronavirus isolate Rs9401, complete genome                                       .T..................................T.....................T....
  29 >KY417147.1 Bat SARS-like coronavirus isolate Rs4237, complete genome                                       .T.............................................................
  30 >AY350750.1 SARS coronavirus PUMC01, complete genome                                                        ...T...........................................................
  31 >KF514404.1 SARS coronavirus wtic-MB strain SARS/VeroE6_lab/USA/WTic_c1.9P20/2010, complete genome          ...............................................................
  32 >KF514420.1 SARS coronavirus ExoN1 strain SARS/VeroE6_lab/USA/ExoN1_c5P10/2009, complete genome             ...............................................................
  33 >FJ882951.1 SARS coronavirus MA15 ExoN1 isolate P3pp3, complete genome                                      ...............................................................
  34 >KF514397.1 SARS coronavirus wtic-MB strain SARS/VeroE6_lab/USA/WTic_c2P10/2009, complete genome            ...............................................................
  35 >JX163923.1 SARS coronavirus isolate Tor2/FP1-10912, complete genome                                        ...............................................................
  36 >JF292910.1 SARS coronavirus MA15 isolate d2ym5, complete genome                                            ...............................................................
  37 >HQ890539.1 SARS coronavirus MA15 ExoN1 isolate d3om1, complete genome                                      ...............................................................
  38 >AY559084.1 SARS coronavirus Sin3765V, complete genome                                                      ...............................................................
  39 >AY613948.1 SARS coronavirus PC4-13, complete genome                                                        ...............................................................
  40 >EU371563.1 SARS coronavirus BJ182-8, complete genome                                                       ...............................................................
  41 >AY323977.2 SARS coronavirus HSR 1, complete genome                                                         ...............................................................
  42 >JF292922.1 SARS coronavirus ExoN1 isolate c5P1, complete genome                                            ...............................................................
  43 >JF292905.1 SARS coronavirus MA15 ExoN1 isolate d3om4, complete genome                                      ...............................................................
  44 >AP006560.1 SARS coronavirus TWS genomic RNA, complete genome                                               ...................T...........................................
  45 >AP006559.1 SARS coronavirus TWK genomic RNA, complete genome                                               ...................T...........................................
  46 >AP006558.1 SARS coronavirus TWJ genomic RNA, complete genome                                               ...................T...........................................
  47 >AY502924.1 SARS coronavirus TW11, complete genome                                                          ...................T...........................................
  48 >AY502932.1 SARS coronavirus TW9, complete genome                                                           ...................T...........................................
  49 >AP006561.1 SARS coronavirus TWY genomic RNA, complete genome                                               ...................T...........................................
  50 >AY502923.1 SARS coronavirus TW10, complete genome                                                          ...................T...........................................
  51 >AY348314.1 SARS coronavirus Taiwan TC3, complete genome                                                    ...................T...........................................
  52 >AY338175.1 SARS coronavirus Taiwan TC2, complete genome                                                    ...................T...........................................
  53 >KP886809.1 Bat SARS-like coronavirus YNLF_34C, complete genome                                             ..................T.G..........................................
  54 >KP886808.1 Bat SARS-like coronavirus YNLF_31C, complete genome                                             ..................T............................................
  55 >FJ882960.1 SARS coronavirus ExoN1 isolate P3pp34, complete genome                                          ...........................G...................................
  56 >GU553363.1 SARS coronavirus HKU-39849 isolate TCVSP-HARROD-00001, complete genome                          ...............................................................
  57 >KF514401.1 SARS coronavirus ExoN1 strain SARS/VeroE6_lab/USA/ExoN1_c5.5P20/2010, complete genome           ...............................................................
  58 >KF514394.1 SARS coronavirus wtic-MB strain SARS/VeroE6_lab/USA/WTic_c1P20/2009, complete genome            ...............................................................
  59 >EA012707.1 Sequence 1 from patent US 7129042                                                               ...............................................................
  60 >CQ918585.1 Sequence 2 from Patent WO2004096842                                                             ...............................................................
  61 >HW375992.1 JP 2012255024-A/1: MODIFIED SMALL INTERFERING RNA MOLECULES AND METHODS OF USE                  ...............................................................
  62 >FJ882940.1 SARS coronavirus ExoN1 isolate P3pp37, complete genome                                          ...............................................................
  63 >AY304495.1 SARS coronavirus GZ50, complete genome                                                          ...............................................................
  64 >AY394991.1 SARS coronavirus HZS2-Fc, complete genome                                                       ...............................................................
  65 >AY559083.1 SARS coronavirus Sin3408, complete genome                                                       ...............................................................
...
 262 >KF514418.1 SARS coronavirus wtic-MB strain SARS/VeroE6_lab/USA/WTic_c3P1/2009, complete genome             ...............................................................
 263 >FJ882962.1 SARS coronavirus MA15 ExoN1 isolate P3pp10, complete genome                                     ...............................................................
 264 >KF514395.1 SARS coronavirus ExoN1 strain SARS/VeroE6_lab/USA/ExoN1_c8P1/2009, complete genome              ...............................................................
 265 >JF292913.1 SARS coronavirus MA15 isolate d4ym3, complete genome                                            ...............................................................
 266 >FJ882961.1 SARS coronavirus MA15 isolate P3pp5, complete genome                                            ........................T......................................
 267 >FJ882931.1 SARS coronavirus ExoN1 isolate P3pp12, complete genome                                          ...........................................................C...
 268 >FJ882955.1 SARS coronavirus ExoN1 isolate P3pp19, complete genome                                          ...........................................................C...
 269 >FJ882959.1 SARS coronavirus MA15 ExoN1 isolate P3pp6, complete genome                                      ..................................................T............
 270 >GU553365.1 SARS coronavirus HKU-39849 isolate TCVSP-HARROD-00003, complete genome                          .........T.....................................................
 271 >AY559095.1 SARS coronavirus Sin847, complete genome                                                        .....................T.........................................
 272 >AY559085.1 SARS coronavirus Sin848, complete genome                                                        .....................T.........................................
 273 >FJ588686.1 Bat SARS CoV Rs672/2006, complete genome                                                        ........................................T......................
 274 >KC881005.1 Bat SARS-like coronavirus RsSHC014, 2013/11/22                                                  ....................................T...T..........C...........
 275 >KC881005.1 Bat SARS-like coronavirus RsSHC014, complete genome                                             ....................................T...T..........C...........
 276 >KY417144.1 Bat SARS-like coronavirus isolate Rs4084, complete genome                                       ....................................T...T..........C...........
 277 >KY417150.1 Bat SARS-like coronavirus isolate Rs4874, complete genome                                       ....................................T...T......................
 278 >KC881006.1 Bat SARS-like coronavirus Rs3367, complete genome                                               ....................................T...T......................
 279 >KT444582.1 SARS-like coronavirus WIV16, complete genome                                                    ....................................T...T......................
 280 >KF367457.1 Bat SARS-like coronavirus WIV1, complete genome                                                 ....................................T...T......................
 281 >KY417149.1 Bat SARS-like coronavirus isolate Rs4255, complete genome                                       ....................................T...T...............G......
 282 >KY417145.1 Bat SARS-like coronavirus isolate Rf4092, complete genome                                       ........................................................G......
 283 >AY345987.1 SARS coronavirus CUHK-AG02, complete genome                                                     ...............................................................
 284 >HQ890536.1 SARS coronavirus MA15 ExoN1 isolate d2om3, complete genome                                      ...............................................................
 285 >KF514413.1 SARS coronavirus wtic-MB strain SARS/VeroE6_lab/USA/WTic_c1.6P20/2010, complete genome          ...............................................................
 286 >AP006557.1 SARS coronavirus TWH genomic RNA, complete genome                                               ...............................................................
 287 >FJ882948.1 SARS coronavirus MA15 isolate P3pp3, complete genome                                            ...............................................................
 288 >AY545917.1 SARS coronavirus isolate HC/GZ/81/03, complete genome                                           ...............................................................
 289 >AY394850.2 SARS coronavirus WHU, complete genome                                                           ...............................................................
 290 >AY559087.1 SARS coronavirus Sin3725V, complete genome                                                      ...............................................................
 291 >AY394995.1 SARS coronavirus HSZ-Cc, complete genome                                                        ...............................................................
 292 >AY394979.1 SARS coronavirus GZ-C, complete genome                                                          ...............................................................
 293 >AY351680.1 SARS coronavirus ZMY 1, complete genome                                                         ...............................................................
 294 >KY770858.1 Bat coronavirus isolate Anlong-103, complete genome                                             ...............................................................
 295 >CS480537.1 Sequence 11 from Patent WO2006136448                                                            ...............................................................
 296 >GP243203.1 Sequence 3 from patent US 7504205                                                               ...............................................................
 297 >AY310120.1 SARS coronavirus FRA, complete genome                                                           ...............................................................
 298 >HZ038027.1 JP 2015091247-A/41: ATTENUATED VIRUSES USEFUL FOR VACCINES                                      ...............................................................
 299 >CS079028.1 Sequence 16 from Patent WO2005035556                                                            ...............................................................
 300 >JQ316196.1 SARS coronavirus HKU-39849 isolate UOB, complete genome                                         ...............................................................
 301 >FJ882936.1 SARS coronavirus wtic-MB isolate P3pp2, complete genome                                         ...............................................................
 302 >AY394986.1 SARS coronavirus HSZ-Cb, complete genome                                                        ...............................................................
 303 >AY595412.1 SARS coronavirus LLJ-2004, complete genome                                                      ...............................................................
 304 >AY545914.1 SARS coronavirus isolate HC/SZ/79/03, complete genome                                           ...............................................................
 305 >FJ882944.1 SARS coronavirus ExoN1 isolate P3pp23, complete genome                                          T..............................................................
 306 >EU371564.1 SARS coronavirus BJ182-12, complete genome                                                      .......C.......................................................
 307 >AY357076.1 SARS coronavirus PUMC03, complete genome                                                        .......-....................T..................................
 308 >AY485277.1 SARS coronavirus Sino1-11, complete genome                                                      .......-....................T..................................
 309 >JF292921.1 SARS coronavirus wtic-MB isolate c1P1, complete genome                                          ...............................................................
 310 >FJ882954.1 SARS coronavirus ExoN1 isolate P3pp46, complete genome                                          ................Y..............................................
 311 >AY345986.1 SARS coronavirus CUHK-AG01, complete genome                                                     ...............................................................
 312 >JX163928.1 SARS coronavirus isolate Tor2/FP1-10895, complete genome                                        ...............................................................
 313 >HQ890534.1 SARS coronavirus MA15 ExoN1 isolate d2om1, complete genome                                      ...............................................................
 314 >HQ890542.1 SARS coronavirus MA15 isolate d2om1, complete genome                                            ...............................................................
 315 >KF514403.1 SARS coronavirus ExoN1 strain SARS/VeroE6_lab/USA/ExoN1_c5.1P20/2010, complete genome           ...............................................................
 316 >AY714217.1 SARS Coronavirus CDC#200301157, complete genome                                                 ...............................................................
 317 >KF514412.1 SARS coronavirus ExoN1 strain SARS/VeroE6_lab/USA/ExoN1_c13P20/2009, complete genome            ...............................................................
 318 >KF514422.1 SARS coronavirus wtic-MB strain SARS/VeroE6_lab/USA/WTic_c1.3P20/2010, complete genome          ...............................................................
 319 >AY864805.1 SARS coronavirus BJ162, complete genome                                                         ...............................................................
 320 >HQ890538.1 SARS coronavirus MA15 ExoN1 isolate d2om5, complete genome                                      ...............................................................
 321 >JF292917.1 SARS coronavirus MA15 isolate d3om2, complete genome                                            ...............................................................
 322 >KF514398.1 SARS coronavirus wtic-MB strain SARS/VeroE6_lab/USA/WTic_c1.10P20/2010, complete genome         ...............................................................
 323 >KF514402.1 SARS coronavirus ExoN1 strain SARS/VeroE6_lab/USA/ExoN1_c5.6P20/2010, complete genome           ...............................................................
 324 >KF514405.1 SARS coronavirus ExoN1 strain SARS/VeroE6_lab/USA/ExoN1_c5.2P20/2010, complete genome           ...............................................................
 325 >HQ890533.1 SARS coronavirus MA15 ExoN1 isolate d4ym3, complete genome                                      ...............................................................
 326 >EA012709.1 Sequence 3 from patent US 7129042                                                               ...............................................................
 327 >JX163925.1 SARS coronavirus isolate Tor2/FP1-10895, complete genome                                        ...............................................................
 328 >JF292912.1 SARS coronavirus MA15 isolate d4ym2, complete genome                                            ...............................................................
 329 >HQ890541.1 SARS coronavirus MA15 isolate d2ym1, complete genome                                            ...............................................................
 330 >AY559082.1 SARS coronavirus Sin852, complete genome                                                        ...............................................................
 331 >AY568539.1 SARS coronavirus GZ0401, complete genome                                                        ...............................................................
 332 >KY417142.1 Bat SARS-like coronavirus isolate As6526, complete genome                                       ..........................................C....................
 333 >MK211378.1 Coronavirus BtRs-BetaCoV/YN2018D, complete genome                                               ..........................................C....................
 334 >MK211376.1 Coronavirus BtRs-BetaCoV/YN2018B, complete genome                                               ..........................................C....................
 335 >KY417146.1 Bat SARS-like coronavirus isolate Rs4231, complete genome                                       .................T........................C......G.............
 336 >FJ882927.1 SARS coronavirus wtic-MB isolate P1pp1, complete genome                                         ...............................................................
 337 >KF514396.1 SARS coronavirus wtic-MB strain SARS/VeroE6_lab/USA/WTic_c3P10/2009, complete genome            ...............................................................
 338 >AY282752.2 SARS coronavirus CUHK-Su10, complete genome                                                     ...............................................................
 339 >AY394984.1 SARS coronavirus HSZ-A, partial genome                                                          ...............................................................
 340 >FJ882938.1 SARS coronavirus wtic-MB, complete genome                                                       ...............................................................
 341 >MK062180.1 SARS coronavirus Urbani isolate icSARS-MA, complete genome                                      ...............................................................
 342 >CS079026.1 Sequence 14 from Patent WO2005035556                                                            ...............................................................
 343 >GX394655.1 Sequence 1 from patent US 7776521                                                               ...............................................................
 344 >GP426726.1 Sequence 13 from patent US 7527926                                                              ...............................................................
 345 >HI553383.1 Sequence 41 from Patent EP2139515                                                               ...............................................................
 346 >MK062183.1 SARS coronavirus Urbani isolate icSARS-C7, complete genome                                      ...............................................................
 347 >AY362699.1 SARS coronavirus TWC3, complete genome                                                          ...............................................................
 348 >FJ882933.1 SARS coronavirus wtic-MB isolate P3pp6, complete genome                                         ...............................................................
 349 >AY394997.1 SARS coronavirus ZS-A, complete genome                                                          ...............................................................
 350 >JF292915.1 SARS coronavirus MA15 isolate d4ym5, complete genome                                            ...............................................................
 351 >FJ882932.1 SARS coronavirus wtic-MB isolate P3pp14, complete genome                                        ...............................................................
 352 >AY613949.1 SARS coronavirus PC4-136, complete genome                                                       ...............................................................
 353 >AY545915.1 SARS coronavirus isolate HC/SZ/DM1/03, complete genome                                          ...............................................................
 354 >FJ882952.1 SARS coronavirus MA15 isolate P3pp4, complete genome                                            ...............................................................
 355 >AY502925.1 SARS coronavirus TW2, complete genome                                                           ...............................................................
 356 >EU371562.1 SARS coronavirus BJ182-4, complete genome                                                       ...............................................................
 357 >MK211374.1 Coronavirus BtRl-BetaCoV/SC2018, complete genome                                                .....................................A.......................T.
 358 >AY357075.1 SARS coronavirus PUMC02, complete genome                                                        ..T............................................................
 359 >AY485278.1 SARS coronavirus Sino3-11, complete genome                                                      ..T............................................................
 360 >AH013708.2 SARS coronavirus Sin0409, partial sequence                                                      ..A............................................................
 361 >AH013709.2 SARS coronavirus Sin_WNV, partial sequence                                                      ..A............................................................
 362 >KY417148.1 Bat SARS-like coronavirus isolate Rs4247, complete genome                                       ..........................................................T....
 363 >AY278489.2 SARS coronavirus GD01, complete genome                                                          ...............A...............................................
 364 >KF514407.1 SARS coronavirus ExoN1 strain SARS/VeroE6_lab/USA/ExoN1_c5.7P20/2010, complete genome           .........................A.....................................
 365 >FJ882956.1 SARS coronavirus ExoN1 isolate P3pp53, complete genome                                          .........................A.....................................
 366 >JX162087.1 SARS coronavirus ExoN1 isolate c5P10, complete genome                                           .........................A.....................................
 367 >AY394981.1 SARS coronavirus HGZ8L1-A, partial genome                                                       ..............................................................T
 368 >KY938558.1 Bat coronavirus strain 16BO133, complete genome                                                 ............G......T.............T..A.T.....C.................T
 369 >KU182964.1 Bat coronavirus isolate JTMC15, complete genome                                                 G...........G......T................A.T..........G......G......
 370 >KJ473811.1 BtRf-BetaCoV/JL2012, complete genome                                                            ............G......T................A.T..........G......G......
 371 >KY770860.1 Bat coronavirus isolate Jiyuan-84, complete genome                                              ............G......T................A...T............TT.T......
 372 >KJ473813.1 BtRf-BetaCoV/SX2013, complete genome                                                            ............G......T................A...T....A.......TT.T......
 373 >DQ648856.1 Bat coronavirus (BtCoV/273/2005), complete genome                                               ............G......T................A...T.......C....TT.T......
 374 >DQ412042.1 Bat SARS coronavirus Rf1, complete genome                                                       ............G......T................A...T.......C....TT.T......
 375 >KJ473812.1 BtRf-BetaCoV/HeB2013, complete genome                                                           ............G......T................A...T............TT.T......



 378 >MN908947.3 Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome                        .....G.............T..........CT.TT.TT..TT.....T...A---........
 380 >MG772933.1 Bat SARS-like coronavirus isolate bat-SL-CoVZC45, complete genome                               .....G........T...............CT.TT.TT..TT.....T...A---......T.
 382 >MG772934.1 Bat SARS-like coronavirus isolate bat-SL-CoVZXC21, complete genome                              .....G........T...............CT.TT.TT..TT.....T...A---......T.



 384 >KY352407.1 Severe acute respiratory syndrome-related coronavirus strain BtKY72, complete genome            ....A........AT.......T.........GT.GTT.ATA.....TC..C.G..CA...T.
 385 >NC_014470.1 Bat coronavirus BM48-31/BGR/2008, complete genome                                              ....A.C......AT.......C...A......G..TT..TAAGCT.TC..C.G.AG..AT..
 386 >GU190215.1 Bat coronavirus BM48-31/BGR/2008, complete genome                                               ....A.C......AT.......C...A......G..TT..TAAGCT.TC..C.G.AG..AT..



   4 >GQ153540.1 Bat SARS coronavirus HKU3-5, complete genome                                                    .....G.....C........................A...TA...........G.........



---Index---------------------------------------------------------------------------------------------------------ACGCGAAGCCTTCTCGTCCCACACCTGAACTAAAACGGCGCGTATCACTTCGAAGGAGCTCCC
-codon-position--------------------------------------------------------------------------------------------------2 1 111222112112 1212 121 1 2121112 1212111 12 112 2 12 12 1221
                                                                                                                 000000000000000000000000000000000000000000000000000000000000000
                                                                                                                 523895813681240159389012714645247345672351723489234678901260149

 

[gsgs]

see the recent nature paper Zhou et.al (preview). they have a table 3 , similarities by region with 22 genomes and 11 regions

 

[Emily]

I copied this post from another thread we have on the site. This is the research paper related to AVP78033.1. We have been looking at this interesting study.



The China scientific community has the genetic material. In this 2018 study they used mammals, and proposed further such studies.

Key word: infectivity


Emerg Microbes Infect. 2018; 7: 154.
Published online 2018 Sep 12. doi: 10.1038/s41426-018-0155-5
PMCID: PMC6135831
PMID: 30209269


Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats


Dan Hu,[SUP]1,[/SUP][SUP]2[/SUP]Changqiang Zhu,[SUP]2[/SUP]Lele Ai,[SUP]2[/SUP]Ting He,[SUP]2[/SUP]Yi Wang,[SUP]3[/SUP]Fuqiang Ye,[SUP]2[/SUP]Lu Yang,[SUP]2[/SUP]Chenxi Ding,[SUP]2[/SUP]Xuhui Zhu,[SUP]2[/SUP]Ruicheng Lv,[SUP]2[/SUP]Jin Zhu,[SUP]2[/SUP]Bachar Hassan,[SUP]4[/SUP]Youjun Feng,[SUP]

[/SUP][SUP]5[/SUP]Weilong Tan,[SUP]

[/SUP][SUP]2[/SUP] and Changjun Wang[SUP]

[/SUP][SUP]1,[/SUP][SUP]2[/SUP]
Author information Article notes Copyright and License information Disclaimer
[SUP]1[/SUP]Department of Epidemiology, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038 China
[SUP]2[/SUP]Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002 China
[SUP]3[/SUP]Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province 214064 P.R. China
[SUP]4[/SUP]Stony Brook University, Stony Brook, 11794 USA
[SUP]5[/SUP]Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
Youjun Feng, Email: nc.ude.ujz@jygnef.
Contributor Information.
[SUP]

[/SUP]Corresponding author.
This article has been cited by other articles in PMC.

Associated Data

Supplementary Materials
Go to: Abstract


SARS coronavirus (SARS-CoV), the causative agent of the large SARS outbreak in 2003, originated in bats. Many SARS-like coronaviruses (SL-CoVs) have been detected in bats, particularly those that reside in China, Europe, and Africa. To further understand the evolutionary relationship between SARS-CoV and its reservoirs, 334 bats were collected from Zhoushan city, Zhejiang province, China, between 2015 and 2017. PCR amplification of the conserved coronaviral protein RdRp detected coronaviruses in 26.65% of bats belonging to this region, and this number was influenced by seasonal changes. Full genomic analyses of the two new SL-CoVs from Zhoushan (ZXC21 and ZC45) showed that their genomes were 29,732 nucleotides (nt) and 29,802 nt in length, respectively, with 13 open reading frames (ORFs). These results revealed 81% shared nucleotide identity with human/civet SARS CoVs, which was more distant than that observed previously for bat SL-CoVs in China. Importantly, using pathogenic tests, we found that the virus can reproduce and cause disease in suckling rats, and further studies showed that the virus-like particles can be observed in the brains of suckling rats by electron microscopy. Thus, this study increased our understanding of the genetic diversity of the SL-CoVs carried by bats and also provided a new perspective to study the possibility of cross-species transmission of SL-CoVs using suckling rats as an animal model.


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135831/

From paper:
"Briefly, each intestinal sample (approximately 0.1 g) was homogenized in a glass grinder with ten volumes of SM buffer (50 mM Tris, 10 mM MgSO4, 0.1 M NaCl, pH 7.5). The homogenate was centrifuged at 12,000 g for 10 min at 4 ?C, but only the supernatant was used"

Paper said this was done at safety level BL-3. USDA standards say:
https://www.ars.usda.gov/northeast-area/docs/she/biological-safety-manual/#BL3
"D. BLENDERS, SONICATORS, MILLS, GRINDERS & CELL SORTERS

These devices release considerable aerosols during operation. For maximum protection to the operator during blending or mixing of infectious materials, the following practices should be observed."
...

"5. Glass blender bowls are undesirable for use with infectious materials because of potential breakage. If used, they should be covered with a polypropylene jar to prevent dispersal of glass in case of breakage."

 

[Pathfinder]

Chinese virologist claims coronavirus derived from 'Zhoushan bat virus'
...
By Keoni Everington, Taiwan News, Staff Writer
2020/08/06 15:02
...
Yan then claimed that she and her team have produced a scientific report that shows the origin of COVID-19 is the "PLA-owned Zhoushan bat coronavirus." She plans to release the report in the near future...

The virologist said Wuhan Institute of Virology (WIV) scientist Shi Zhengli, also known as "Bat Woman," deliberately posted a paper on Feb. 3 to draw attention to a coronavirus strain identified as RaTG13...Yan claims this was an orchestrated attempt to throw investigators off the Zhoushan bat virus strains...

When asked if the Zhoushan strain is in the PLA's catalog of viruses and if COVID-19 resulted from gain-of-function or other manipulations in the WIV, Yan said the virus could have come from any one of the PLA's numerous labs, such as in Hong Kong, Shanghai, or Harbin.
...
Yan said that when she worked on vaccines and virus function testing in Chinese labs and carried out virus replication, "We never made just one type of virus we make a lot of strains of virus and stocked them and then later we would test their function, test their characteristics."

Yan emphasized that COVID-19 is not from nature, but rather it is "lab-modified."
...

https://www.taiwannews.com.tw/en/news/3981833

 

[JJackson]

I am not sure what they are calling a grinder and what is a blender. a grinder I would expect to be two ground glass surfaces, as you might find on a reagent bottle or drinks decanter's stopper. a blender would be rotating blades as in a liquidiser. In either event nothing would get into a BSL3 lab to perform that function that was not designed to perform it to a BSL3 safety level.

 

[JJackson]

The E protein is the smallest of the structural proteins (about 75aa) and seems to perform multiple function in various configurations. It can form monomers, dimers, trimers and pentamers which must put considerable biological constraints on its ability to change sequence without impacting fitness. In addition the central section is hydrophobic with hydrophilic terminal domains. Its terminal domains are involved in anchoring it to the ER-Golgi complex and it is critical in correct viral assembly. It also seems to have a roll in aligning and curving the M protein, which makes the viral capsid, to give the virus its spherical shape. When knocked out viruses can not escape the host cell as they are held in phospholipid bi-layer by an umbilical that E is assumed to cut. The homopentameric form is an ion pump analogous the that created by the M2 protein in influenza.

 

[Emily]

So the grinding and centrifuging was done in the study above to process infected bat tissue that was somehow forced into the brains of baby rats.

Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats
"To test the pathogenicity of the ZC45 agent, infection experiments were performed in suckling rats. 3-day-old suckling BALB/c rats (SLAC, China) were intracerebrally inoculated with 20 μl of volume grinding supernatant of ZC45 intestinal tissue."

That's high risk invasive animal research. Reminded me of Gajduseck's work.
https://journals.lww.com/aidsonline...experiments_triggered_the_emergence_of.2.aspx
Kuru experiments triggered the emergence of pathogenic SIV[SUB]mac[/SUB]
"In this context, several questions remain to be addressed to understand the mechanism(s) of emergence of pathogenic viruses following cross-species transmission: Why is SIV[SUB]mac239[/SUB] highly pathogenic in Rh? What were the circumstances of the emergence of this pathogenic virus? What are the requirements for a cross-transmitted virus to become pathogenic in a new host?

The answers to these questions are not easy to obtain because the emergence of pathogenic SIV[SUB]mac[/SUB] occurred in the 1970s and it was not until the mid 1980s that the virus was discovered, by which point it had already reached its full pathogenic potential. However, we have collected and reassembled data that strongly suggest that highly invasive experimental manipulations, rather than casual contact, inadvertently gave rise to the highly pathogenic SIV[SUB]mac[/SUB]isolate, used in AIDS research from the 1980s to the present time."

Why did they adapt a SARS-like bat virus to rats and in such a way to train it to infect so many different tissue types?

https://www.nature.com/articles/166910b0
Intracerebral Inoculation of Mice: Fate of the Inoculum
"IT has long been known that a virus may become widely disseminated following intracerebral inoculation into an experimental animal."

I think that somehow this adapted virus spread among lab animals, evolving silently until ultimately infecting a human.

 

[Pathfinder]

Article
Open Access
Published: 03 February 2020

A new coronavirus associated with human respiratory disease in China

Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Zhi-Gang Song, Yi Hu, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei, Ming-Li Yuan, Yu-Ling Zhang, Fa-Hui Dai, Yi Liu, Qi-Min Wang, Jiao-Jiao Zheng, Lin Xu, Edward C. Holmes & Yong-Zhen Zhang
...
Notably, WHCV is most closely related to bat coronaviruses, and shows 100% amino acid similarity to bat SL-CoVZC45 in the nsp7 and E proteins (Supplementary Table 3)
...
https://www.nature.com/articles/s41586-020-2008-3

 

[JJackson]

Emily
I had a quick read through the SL-CoV paper you linked to and in answer to you question
"Why did they adapt a SARS-like bat virus to rats and in such a way to train it to infect so many different tissue types?"
I do not think they did. They found they could infect a Vero E6 cell which can be made to express a human ACE2 receptor but there are many other steps beyond cell entry before the host cell can start shedding infectious virions and the Vero cells lacked the ability to perform one or more of them so no infectious virus was produced. They then moved to rats as their animal model and the rats did produce infectious virus. However rats, and mice do not make very good models of human infection as the virus behaves quite differently, in terms of its pathology, and causes death by infecting the brain, also they have reduced (not increased) body temperature and do not sneeze or cough so make poor subjects for respiratory transmission. The virus was not modified get it to display these tissue tropisms it is just the effect it has on rats. In us the SARS-Cov-2 transmission route is currently thought to be first URT followed by movement to the LRT and that in most patients it is mainly localised here without systemic spread. There is some evidence that in some cases it does get into other areas if this is the case then it may be the cause of some of the late stage sequelae and/or apparent reinfection/recurrences.
I do not know enough about retroviruses to comment on SIV but it was a long time ago so lab procedures and safety protocols are entirely different.
The link is to lab suppliers range of homogenisers, with pictures, so you can see what they are.
https://www.thomassci.com/scientific...ue-Homogenizer
This is a detailed look inside a BSL4 facility showing the level of containment required.
https://www.microbe.tv/twiv/twiv-654

Edit -Afterthought
Your earlier question made me think about what effect a blender - in the kitchen blender sense - would have on a virus. If you put water on the blender it just flows around the blades unharmed, if you put peas in it homogenises them but what about the virions? Would they flow around the blades and if so how could you redesign the blender.
Grain of salt - 3x10[SUP]-4[/SUP] meters
Human eye resolution - 5x10[SUP]-5[/SUP]
HeLa cell - 5x10[SUP]-7[/SUP]
Virion - 1x10[SUP]-7[/SUP]
H[SUB]2[/SUB]O - 2x10[SUP]-10[/SUP]

 

[Emily]

JJackson,

This is a well written paper but it covers a lot of ground with some historical studies described so I want to clear up a couple of things.

1. The research was done at BSL 3, not BSL 4. BSL 4 would have been better, but the BSL 4 lab was not completed when this work was done.

2. "They found they could infect a Vero E6 cell which can be made to express a human ACE2 receptor”

   They could not infect Vero cells in this study with the two new SL-CoVs from Zhoushan (ZXC21 and ZC45). You were reading the historical section about work done in 2013: “Notably, during longitudinal surveillance of the Rhinolophus sinicus colony in the Yunnan Province of China over the past few years, a Chinese research team successfully isolated a live SL-CoV sample from Vero E6 cells that were incubated in the bat feces in 2013” The bats in this paper’s research were collected in 2015-2017.
3. The adaptation of the virus to rats was done by forcing the liquefied bat intestines into the rat pups brains. Totally unnatural and just as dangerous as in Gajuseck’s day in terms of the biology.

I don’t buy the paper’s justification for doing this work considering the endangering of the human population and the animal suffering involved. I think the contrived, invasive brain inoculation was done for the purpose of job security: “These findings strongly suggest the need for continued surveillance of viruses originating from wild animals and promote further research to study the possibility of cross-species transmission of these viruses.”

Interesting, too, that there was only one American researcher involved in this study and he did another study as the sole American with the PLA while affiliated with UNC Chapel Hill, (where gain-function research was done in the past and where a researcher was just bitten by a SARS-Cov-2 infected mouse). Seems the same old publicly-funded, self-justifying, crowd reassuring us that all is well.