Use:

Checks to see if a flu HA sequence belongs to a high path flu or a low path flu strain.

This program checks patterns that other people have found (Zhirnov, Ikizler, and Wright 2002 from Walker et al., 1992; Kalthoff, Globig, Beer 2009) to distinguish between high path and low path flu strains. Each pattern starts from the P1' site (first amino acid in HA2) and ends with the P3 site (P1'-P1-P2-P3). The output tells if the strain was a high (high_path) or low (low_path) strain. The output also prints out the P1 to P6 amino acids and if there was a Phenylalanine or Tryosine at the P2. Sun et al., 2010 found a Phenylalanine or Tryosine at the P2 position made at least one low path H1N1 more virulant.

List of patterns used to find if a strain is high path:

• P1'-R-R
• P1'-R-K
• P1'-R-X-R
• P1'-R-X-K

The one warning I will give is that this program is only as good as the patterns I have chosen to check. If I am wrong on a pattern or missed a pattern, then the results will be wrong. So, double check the P1 to P6 amino acids printed out to make sure they line up with the high/low path result.

Also, I should note that I am not a flu person. I just heard people might be interested in a program like this. And that there used to be one, but it disappeared.

This code is licensed under two licenses, the unlicense (public domain license) or MIT in cases were the unlicense can not be used. You are free to choose the license you want.

Updates

20240627: Updated the waterman aligner and changed some of the coding style. The complied program name is shorter (getHaPath). The python library support has not been updated and so is no longer present. See 2024-03-21-code for the old version.

20240321: I fixed a minor error in my codon table "hiLowPathTbls.h" were Phenylalanine was confused with Luecine (one case). I also changed this code to compile with the c89 standard instead of c99 and added in an install option for Mac make mac (no idea if it works). I also removed -static from the python library.

References

Kalthoff D, Globig A, Beer M. (Highly pathogenic) avian influenza as a zoonotic agent. Vet Microbiol. 2010 Jan 27;140(3-4):237-45. doi: 10.1016/j.vetmic.2009.08.022. Epub 2009 Aug 26. PMID: 19782482.

Sun X, Tse LV, Ferguson AD, Whittaker GR. Modifications to the hemagglutinin cleavage site control the virulence of a neurotropic H1N1 influenza virus. J Virol. 2010 Sep;84(17):8683-90. doi: 10.1128/JVI.00797-10. Epub 2010 Jun 16. PMID: 20554779; PMCID: PMC2919019.

Walker JA, Sakaguchi T, Matsuda Y, Yoshida T, Kawaoka Y. Location and character of the cellular enzyme that cleaves the hemagglutinin of a virulent avian influenza virus. Virology. 1992 Sep;190(1):278-87. doi: 10.1016/0042-6822(92)91214-f. PMID: 1529533.

Zhirnov OP, Ikizler MR, Wright PF. Cleavage of influenza a virus hemagglutinin in human respiratory epithelium is cell associated and sensitive to exogenous antiproteases. J Virol. 2002 Sep;76(17):8682-9. doi: 10.1128/jvi.76.17.8682-8689.2002. PMID: 12163588; PMCID: PMC136409.

Building isHiLowPathFlu

Mac/building non-static

make mac
sudo make install

Building static

make
sudo make install

Using getHaPath:

Using the standalone

This program has three options, but only one of the three options is needed. The only required option is the fasta file (-fa) to get the HA sequence from. This program will align each sequence in the fasta file to an consensus of the last 3 bases of H1 and the first 54 bases of the HA2 gene ("arrGGNHTNYHNrGNGCNDWHrYNrKNYKBAT"). However, this is only as good as my consensus, so it will likely fail at times. To fix this issue you can upload a feature table or input the position of the first base (index 1) in the HA2 gene (P1' position).

If you are inputting a feature table or the first base in HA2, then only one HA sequence is processed. You also will need to mark the HA sequence in the fasta file with HA in the header (Line with an >), otherwise this program will not extract the HA sequence.

The second option is either to use a feature table to get the HA2 starting position from (-tbl) or to manually input the HA2 starting position (-HA2-Start) (as index 1). The feature table should be made and downloaded from https://www.ncbi.nlm.nih.gov/genomes/FLU/annotation/. Just make sure you correct any errors in the HA sequence before hand.

getHaPath -fa HA.fasta;

# or

getHaPath -fa HA.fasta -tbl HA-feature-table.tbl;

# or

getHaPath -fa HA.fasta -HA2Start 1026;

Using this code in C

There are two main .h files in this code you will needed to know about. The first is haPath.c/h, which contains the functions to get the amino acids and determines if a result matches a pattern. The second is haStart.h, which is used to get the HA2 starting position from a feature table and to find the HA sequence in a fasta file.

All the other files are dependencies these two .h files depend on. Or in the case of some files in generalLib, stuff I was to lazy to delete (copied from getDIids).

haStart.c/h

haStart.c/h is set up to find the starting position of the HA2 ORF in the sequence. You can use find_haStart (fun03 haStart.c/h) to find the starting position using a Waterman Smith alignment.

• Input:
  • seqStruct with sequence to get get HA2 postion
    • free with freeHeap_seqST(); fun09 memwater/seqST.c/h
    • read in fasta sequence with getFqSeq_seqST() (fun03 memwater/seqST.c/h)
      • Input: file and seqStruct
      • returns 0 for success
      • returns 1 (def_EOF_seqST) for EOF
      • other values are errors
  • alnSet structure with the alignment settings
  • variable to hold start of HA2 ORF in sequence
  • variable to hold first HA2 mapped base in sequence

haPath.c/h

haPath.c/h converts the HA2 P1 to P6 positions into amino acids with getP1_P6AA_haPath (fun03).

• Input:

  • seqStruct with the HA sequence and position
  • array to hold P1 to P6 positions (length is 7)
  • first base (index 0) in HA2
    • use find_haStart (fun02 haStart.c/h) to get this

• Output:

  • adds P1 to P6 aa sequences to input P1 to P6 array

You can then use the P1 to P6 array and find_haPath (fun02 haPath.h) to detect hi path HA sequences.

• Input:

  • P1 to P6 array used with getP1_P6AA_haPath

• Output:

  • returns 1 if was a high path sequence

Thanks

• To my dad how continues to be a source of encouragement and support.
• To Eric Bortz (one of my mentors) for mentioning that this might be a good idea to code up. And also provided insight into how to determine if a flu was high path or low path.
• NCBI genbank for having a resource were I could grab a couple example flu genomes from.
• Who knows how many answered questions on stack overflow or web tutorials people have posted up. I never asked the questions, but I benefit from other people asking. Thanks to all the people who took time to answer a question, ask a question, or post a tutorial.