Analyzing Genomes from Different Countries
Analyzing Genomes from Different Countries
Pull the data from the data repository
In[]:=
geneticdata=ResourceData["Genetic Sequences of 2019-2020 Wuhan Coronavirus Outbreak"]
Out[]=
First, I chose to compare 2 sequences from China, 1 sequence from the United States, and 1 sequence from Australia with the reference sequence.
First, I chose to compare 2 sequences from China, 1 sequence from the United States, and 1 sequence from Australia with the reference sequence.
Extract the sequences from data
In[]:=
china1=Normal[geneticdata][[8]]["Sequence"];china2=Normal[geneticdata][[25]]["Sequence"];australia=Normal[geneticdata][[5]]["Sequence"];unitedstates=Normal[geneticdata][[15]]["Sequence"];refseq=Normal[geneticdata][[36]]["Sequence"];
Since these genomes are going to be practically identical, an important factor is also when this virus was collected and sampled to see how much the virus mutated over time.
Out[]=
Reference Sequence | China | |
Sequence 1 | China | |
Sequence 2 | China | |
Sequence 3 | Australia | |
Sequence 4 | United States |
Perform alignment and create visuals
In[]:=
tables[{refseq,{china1,china2,australia,unitedstates}}]
Out[]=
| |||||||||||||||||||||||||||||||||||||||||||||||||
| |||||||||||||||||||||||||||||||||||||||||||||||||
Global Alignment Local Alignment |
As you can see, these sequences are practically perfectly identical, as expected. It is interesting to note that the genomes collected later in January (2-4) had more differences with the reference sequence that was first collected in December than the genome collected on December 30 (Sequence 1).
Comparing 2019-nCov with SARS and MERS
Comparing 2019-nCov with SARS and MERS
I also wanted to see how the 2019 - nCov would compare to the SARS virus of 2003 and the MERS virus of 2012. I used the NCBI Gene Bank and the "Import FASTA" function from the repository to get the genetic data for those two viruses.
Import sequence data for SARS and MERS
In[]:=
sars=First@ResourceFunction["ImportFASTA"]["NC_004718.3"][[2]];
In[]:=
mers=First@ResourceFunction["ImportFASTA"]["NC_019843.3"][[2]];
This is the result for the comparison:
Perform alignment and create visuals
In[]:=
tables[{refseq,{sars,mers}}]
Out[]=
| ||||||||||||||||||||||||||||||||
| ||||||||||||||||||||||||||||||||
Global Alignment Local Alignment |
The SARS virus is a lot more similar to the 2019-nCov than the MERS virus. Even though they do have a high level of alignment, as scientists have determined, there is enough genetic difference to label the Wuhan virus as a “novel coronavirus” .