# Multiple-Hit capacity in SARS-CoV-2 Last update 3/4/2021 > **Data in:** > /home/aglucaci/FMM_SARS2/2021/SARS-CoV-2 > /home/aglucaci/FMM_SARS2/2021/SARS-CoV-2/data/fasta/1 > ## Data curation ![](https://i.imgur.com/qegU2UE.png) # Ran through a modified version of SARS2 pipeline https://github.com/veg/SARS-CoV-2/tree/master * submit_job.sh * Modified data directory * fdate=1 * nprocs=2 * extract_genes.sh * Stopped before selection analyses * Creates rapidnj tree Scripts for MH and other selection analyses. > /home/aglucaci/FMM_SARS2/2021/SARS-CoV-2/scripts/run_FMM_v2.sh (this script runs FMM and SLAC) > /home/aglucaci/FMM_SARS2/2021/SARS-CoV-2/scripts/run_BS-MH.sh (This runs BUSTEDS, BUSTEDS-MH, aBSREL, aBSREL-MH) ## Results Top sites of interest * Spike site 70, physiochemical change (Y->L->T->V(bat, nonsyn)->V(bat to human, syn)) * Spike site 325, serine exchange * Spike site 450, G->N(non-syn)->N(syn) * Nucleocapsid site 267, biological DH (1+2) (Q {pangolin, bat} to A in human), review if it is potentially misaligned? * nsp4 site 184, serine island conversion (TH) in pangolins * nsp4 site 81, serine island conversion (DH) in pangolins Comments on other sites * Spike site 860, Q is probably a sequencing error. * Spike site 861, abiological DH (1+3), preserving L, K is probably a sequencing error. * Spike site 1093, A is probably a sequencing error. * Spike site 1145, abiological DH (1+3), preserving L. * Envelope site 51, abiological DH (1+3), preserving L. * Leader site 31, abiological DH (1+3), human F->V in human. ### Spike **{HTML}** <iframe src="https://data.hyphy.org/web/MH_SARS2/compressed_ER_S.html" width="1000" height="600" frameBorder="0"> </iframe> **{Input}** | | 0 | |:--------------------|:---------------------------| | file name | sequences.S.compressed.fas | | number of sequences | 30 | | number of sites | 1273 | | partition count | 1 | **{Test Results}** | | LRT | p-value | |:--------------------------------|---------:|------------:| | Double-hit vs single-hit | 189.862 | 0 | | Triple-hit vs Triple-hit-island | 35.1287 | 3.08625e-09 | | Triple-hit vs double-hit | 37.867 | 5.98817e-09 | | Triple-hit vs single-hit | 227.729 | 0 | | Triple-hit-island vs double-hit | 2.7383 | 0.0979689 | **{Site Substitutions}** | Site\From Codon | GGT | TTA | AGT | TAC | TCT | AAT | GTC | GTT | TAT | GGA | GGG | CTG | TTG | |------------------:|:--------|:--------|:--------|:----------------------|:--------|:---------------|:--------|:---------------|:--------|:--------|:---------------|:--------|:---------------| | 13 | . | . | ['TCA'] | . | . | . | . | . | . | . | . | . | . | | 28 | . | . | . | ['GAT', 'TAT', 'TTC'] | . | . | . | . | . | . | . | . | . | | 70 | . | . | . | . | . | . | ['GTT'] | ['ACA', 'TAT'] | ['CTA'] | . | . | . | . | | 72 | . | . | . | . | . | . | . | . | . | ['TAT'] | ['ACT', 'GGA'] | . | . | | 162 | . | . | ['TCT'] | . | . | . | . | . | . | . | . | . | . | | 325 | . | . | . | . | ['AGT'] | . | . | . | . | . | . | . | . | | 450 | ['AAT'] | . | . | . | . | ['AAC', 'GGT'] | . | . | . | . | . | . | . | | 860 | . | . | . | . | . | . | . | ['CAA'] | . | . | . | . | . | | 861 | . | . | . | . | . | . | . | . | . | . | . | ['CTA'] | ['AAG', 'CTG'] | | 1093 | ['GCC'] | . | . | . | . | . | . | . | . | . | . | . | . | | 1145 | . | ['CTT'] | . | . | . | . | . | . | . | . | . | . | . **{SLAC}** ![](https://i.imgur.com/HqWL5hv.png) ![](https://i.imgur.com/ElWEcS0.png) ![](https://i.imgur.com/sbgzRlV.png) ![](https://i.imgur.com/9sLsduA.png) ![](https://i.imgur.com/R0pdWCB.png) ![](https://i.imgur.com/cowB3IR.png) ![](https://i.imgur.com/BQoPQ0J.png) ![](https://i.imgur.com/MpvNtrj.png) ![](https://i.imgur.com/x6XzoYr.png) ![](https://i.imgur.com/aAIw0N9.png) ![](https://i.imgur.com/c9Y1ADm.png) ### Envelope **{HTML}** <iframe src="https://data.hyphy.org/web/MH_SARS2/compressed_ER_E.html" width="1000" height="600" frameBorder="0"> </iframe> **{Input}** | | 0 | |:--------------------|:---------------------------| | file name | sequences.E.compressed.fas | | number of sequences | 6 | | number of sites | 75 | | partition count | 1 | **{Test Results}** | | LRT | p-value | |:--------------------------------|-------------:|----------:| | Double-hit vs single-hit | 4.37694 | 0.0364284 | | Triple-hit vs Triple-hit-island | -0.000331066 | 1 | | Triple-hit vs double-hit | -0.000276162 | 1 | | Triple-hit vs single-hit | 4.37666 | 0.223559 | | Triple-hit-island vs double-hit | 5.49044e-05 | 0.994088 | **{Site Substitutions}** | Site\From Codon | CTT | |------------------:|:--------| | 51 | ['TTA'] | **{SLAC}** ![](https://i.imgur.com/HfHYFKG.png) ### Nucleocapsid **{HTML}** <iframe src="https://data.hyphy.org/web/MH_SARS2/compressed_ER_N.html" width="1000" height="600" frameBorder="0"> </iframe> **{Input}** | | 0 | |:--------------------|:---------------------------| | file name | sequences.N.compressed.fas | | number of sequences | 24 | | number of sites | 419 | | partition count | 1 | **{Test Results}** | | LRT | p-value | |:--------------------------------|-------------:|------------:| | Double-hit vs single-hit | 14.1241 | 0.000171134 | | Triple-hit vs Triple-hit-island | 0.0787973 | 0.778934 | | Triple-hit vs double-hit | 0.0788147 | 0.961359 | | Triple-hit vs single-hit | 14.2029 | 0.00264152 | | Triple-hit-island vs double-hit | 1.74043e-05 | 0.996671 | **{Site Substitutions}** | Site\From Codon | GCA | |------------------:|:--------| | 267 | ['CAA'] | **{SLAC}** ![](https://i.imgur.com/y0Tzsp3.png) ### Leader **{HTML}** <iframe src="https://data.hyphy.org/web/MH_SARS2/compressed_ER_leader.html" width="1000" height="600" frameBorder="0"> </iframe> **{Input}** | | 0 | |:--------------------|:--------------------------------| | file name | sequences.leader.compressed.fas | | number of sequences | 12 | | number of sites | 180 | | partition count | 1 | **{Test Results}** | | LRT | p-value | |:--------------------------------|-------------:|------------:| | Double-hit vs single-hit | 19.871 | 8.28476e-06 | | Triple-hit vs Triple-hit-island | 0.246531 | 0.619529 | | Triple-hit vs double-hit | 0.246481 | 0.884051 | | Triple-hit vs single-hit | 20.1175 | 0.000160487 | | Triple-hit-island vs double-hit | -5.00444e-05 | 1 | **{Site Substitutions}** | Site\From Codon | TTT | |------------------:|:--------| | 31 | ['GTA'] | **{SLAC}** ![](https://i.imgur.com/3yYMpLF.png) ### nsp3 **{HTML}** <iframe src="https://data.hyphy.org/web/MH_SARS2/compressed_ER_nsp3.html" width="1000" height="600" frameBorder="0"> </iframe> **{Input}** | | 0 | |:--------------------|:------------------------------| | file name | sequences.nsp3.compressed.fas | | number of sequences | 34 | | number of sites | 1950 | | partition count | 1 | **{Test Results}** | | LRT | p-value | |:--------------------------------|---------:|------------:| | Double-hit vs single-hit | 49.0844 | 2.45193e-12 | | Triple-hit vs Triple-hit-island | 1.11283 | 0.291467 | | Triple-hit vs double-hit | 3.4303 | 0.179937 | | Triple-hit vs single-hit | 52.5147 | 2.32656e-11 | | Triple-hit-island vs double-hit | 2.31746 | 0.127929 | **{Site Substitutions}** | Site\From Codon | GGT | GTT | ACT | |------------------:|:--------|:--------|:--------| | 255 | . | ['ATC'] | . | | 674 | ['GTA'] | . | . | | 677 | . | . | ['TTT'] | | 1428 | ['CGA'] | . | . | **{SLAC}** ![](https://i.imgur.com/kKU8p0I.png) ![](https://i.imgur.com/IIxd8W2.png) ![](https://i.imgur.com/A7AZPNF.png) ![](https://i.imgur.com/AAxVXIG.png) ### nsp4 **{HTML}** <iframe src="https://data.hyphy.org/web/MH_SARS2/compressed_ER_nsp4.html" width="1000" height="600" frameBorder="0"> </iframe> **{Input}** | | 0 | |:--------------------|:------------------------------| | file name | sequences.nsp4.compressed.fas | | number of sequences | 13 | | number of sites | 500 | | partition count | 1 | **{Test Results}** | | LRT | p-value | |:--------------------------------|-------------:|------------:| | Double-hit vs single-hit | 28.6135 | 8.83656e-08 | | Triple-hit vs Triple-hit-island | -9.56697e-05 | 1 | | Triple-hit vs double-hit | 4.61787 | 0.0993671 | | Triple-hit vs single-hit | 33.2313 | 2.87837e-07 | | Triple-hit-island vs double-hit | 4.61796 | 0.0316388 | **{Site Substitutions}** | Site\From Codon | TTG | AGT | |------------------:|:---------------|:--------| | 81 | . | ['TCT'] | | 106 | ['CTT', 'TTA'] | . | | 184 | . | ['TCA'] | **{SLAC}** ![](https://i.imgur.com/z0KEo80.png) ![](https://i.imgur.com/Lj3gWYT.png) ![](https://i.imgur.com/YlNvuKO.png) ### nsp8 **{HTML}** <iframe src="https://data.hyphy.org/web/MH_SARS2/compressed_ER_nsp8.html" width="1000" height="600" frameBorder="0"> </iframe> **{Input}** | | 0 | |:--------------------|:------------------------------| | file name | sequences.nsp8.compressed.fas | | number of sequences | 9 | | number of sites | 198 | | partition count | 1 | **{Test Results}** | | LRT | p-value | |:--------------------------------|-------------:|-----------:| | Double-hit vs single-hit | 8.63568 | 0.00329643 | | Triple-hit vs Triple-hit-island | -5.11222e-05 | 1 | | Triple-hit vs double-hit | 4.88553e-05 | 0.999976 | | Triple-hit vs single-hit | 8.63573 | 0.0345474 | | Triple-hit-island vs double-hit | 9.99775e-05 | 0.992022 | **{Site Substitutions}** | Site\From Codon | AGT | |------------------:|:--------| | 85 | ['ATG'] | **{SLAC}** ![](https://i.imgur.com/b0x7I7U.png) ### nsp9 **{HTML}** <iframe src="https://data.hyphy.org/web/MH_SARS2/compressed_ER_nsp9.html" width="1000" height="600" frameBorder="0"> </iframe> **{Input}** | | 0 | |:--------------------|:------------------------------| | file name | sequences.nsp9.compressed.fas | | number of sequences | 4 | | number of sites | 113 | | partition count | 1 | **{Test Results}** | | LRT | p-value | |:--------------------------------|-------------:|------------:| | Double-hit vs single-hit | 13.3441 | 0.000259234 | | Triple-hit vs Triple-hit-island | -0.000424736 | 1 | | Triple-hit vs double-hit | 0.288714 | 0.865579 | | Triple-hit vs single-hit | 13.6328 | 0.00345001 | | Triple-hit-island vs double-hit | 0.289139 | 0.590773 | **{Site Substitutions}** | Site\From Codon | AGT | |------------------:|:--------| | 59 | ['TCT'] | **{SLAC}** ![](https://i.imgur.com/oGbd9Wi.png) ## RSCU ### Spike