Mapping of reads to selected viruses in DAMIAN results (version 2)

Prepare input raw data

# -- Ringversuch --
~/DATA/Data_Damian/241213_VH00358_120_AAG523FM5_Ringversuch
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20579/01_RV1_DNA_S1_R1_001.fastq.gz RV1_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20579/01_RV1_DNA_S1_R2_001.fastq.gz RV1_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20580/02_RV2_DNA_S2_R1_001.fastq.gz RV2_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20580/02_RV2_DNA_S2_R2_001.fastq.gz RV2_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20581/03_RV3_DNA_S3_R1_001.fastq.gz RV3_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20581/03_RV3_DNA_S3_R2_001.fastq.gz RV3_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20582/04_RV4_DNA_S4_R1_001.fastq.gz RV4_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20582/04_RV4_DNA_S4_R2_001.fastq.gz RV4_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20583/05_RV5_DNA_S5_R1_001.fastq.gz RV5_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20583/05_RV5_DNA_S5_R2_001.fastq.gz RV5_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20584/06_RV6_DNA_S6_R1_001.fastq.gz RV6_DNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20584/06_RV6_DNA_S6_R2_001.fastq.gz RV6_DNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20585/07_RV1_RNA_S7_R1_001.fastq.gz RV1_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20585/07_RV1_RNA_S7_R2_001.fastq.gz RV1_RNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20586/08_RV2_RNA_S8_R1_001.fastq.gz RV2_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20586/08_RV2_RNA_S8_R2_001.fastq.gz RV2_RNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20587/09_RV3_RNA_S9_R1_001.fastq.gz RV3_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20587/09_RV3_RNA_S9_R2_001.fastq.gz RV3_RNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20588/10_RV4_RNA_S10_R1_001.fastq.gz RV4_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20588/10_RV4_RNA_S10_R2_001.fastq.gz RV4_RNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20589/11_RV5_RNA_S11_R1_001.fastq.gz RV5_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20589/11_RV5_RNA_S11_R2_001.fastq.gz RV5_RNA_R2.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20590/12_RV6_RNA_S12_R1_001.fastq.gz RV6_RNA_R1.fastq.gz
ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20590/12_RV6_RNA_S12_R2_001.fastq.gz RV6_RNA_R2.fastq.gz

Prepare virus database and select 8 representatives for the eight given viruses from the database

# -- Download all genomes --
# enterovirus D68
# HSV-1
# HSV-2
# Influenza A H1N1
# Cytomegalovirus AD169 (The genome size of Human herpesvirus 5 (HHV-5) — more commonly known as Cytomegalovirus (CMV))
# Influenza A H3N2
# Monkeypox
# HIV-1

esearch -db nucleotide -query "txid42789[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_42789_ncbi.fasta
python ~/Scripts/filter_fasta.py genome_42789_ncbi.fasta complete_42789_ncbi.fasta    #899
esearch -db nucleotide -query "txid10298[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10298_ncbi.fasta
python ~/Scripts/filter_fasta.py genome_10298_ncbi.fasta complete_10298_ncbi.fasta    #162
esearch -db nucleotide -query "txid10310[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10310_ncbi.fasta
python ~/Scripts/filter_fasta.py genome_10310_ncbi.fasta complete_10310_ncbi.fasta    #33
esearch -db nucleotide -query "txid1323429[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_1323429_ncbi.fasta
python ~/Scripts/filter_fasta2.py genome_1323429_ncbi.fasta complete_1323429_ncbi.fasta    #465
esearch -db nucleotide -query "txid10360[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10360_ncbi.fasta
python ~/Scripts/filter_fasta2.py genome_10360_ncbi.fasta complete_10360_ncbi.fasta    #1
esearch -db nucleotide -query "txid41857[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_41857_ncbi.fasta
python ~/Scripts/filter_fasta2.py genome_41857_ncbi.fasta complete_41857_ncbi.fasta    #120
esearch -db nucleotide -query "txid10244[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10244_ncbi.fasta
python ~/Scripts/filter_fasta.py genome_10244_ncbi.fasta complete_10244_ncbi.fasta    #2525
esearch -db nucleotide -query "txid11676[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_11676_ncbi.fasta
python ~/Scripts/filter_fasta.py genome_11676_ncbi.fasta complete_11676_ncbi.fasta    #485995-->7416

# ---- Alternatively, using ENA instead to download the genomes ----
# https://www.ebi.ac.uk/ena/browser/view/11676 (1138065 records)
# #Click "Sequence" and download "Counts" (1132648) and "Taxon descendants count" (1138065) if there is enough time! Downloading time points is 09.04.2025.
# python ~/Scripts/filter_fasta.py  ena_11676_sequence.fasta complete_11676_ena.fasta  #1138065-->????

# Virus Name    NCBI TaxID
# ------------------------
# Enterovirus D68   42789                             >PQ895337.1 Enterovirus D68 isolate SH2024-25870
# HSV-1 (Herpes Simplex Virus 1)    10298             >PQ569920.1 Human alphaherpesvirus 1 isolate MacIntyre, complete genome
# HSV-2 (Herpes Simplex Virus 2)    10310             >OM370995.1 Human alphaherpesvirus 2 strain G, complete genome

    samtools faidx complete_42789_ncbi.fasta PQ895337.1 > Enterovirus_D68_isolate_SH2024-25870.fasta
    samtools faidx complete_10298_ncbi.fasta PQ569920.1 > HSV-1_isolate_MacIntyre.fasta
    samtools faidx complete_10310_ncbi.fasta OM370995.1 > HSV-2_strain_G.fasta

# Influenza A virus (H1N1)  1323429
# The Influenza A virus (H1N1) genome is composed of eight single-stranded negative-sense RNA segments, and the total genome size is approximately 13,500 nucleotides (13.5 kb).
# Segment   Gene    Protein Product(s)  Approx. Length (nt)
# 1 PB2 Polymerase basic 2  ~2,341
# 2 PB1 Polymerase basic 1, PB1-F2  ~2,341
# 3 PA  Polymerase acidic   ~2,233
# 4 HA  Hemagglutinin   ~1,778
# 5 NP  Nucleoprotein   ~1,565
# 6 NA  Neuraminidase   ~1,413
# 7 M   Matrix proteins (M1, M2)    ~1,027
# 8 NS  Nonstructural (NS1, NS2)    ~890

# >LC662544.1 Influenza A virus (H1N1) A/PR/8/34 NEP, NS1 genes for nonstructural protein 2, nonstructural protein 1, complete cds
# >LC662543.1 Influenza A virus (H1N1) A/PR/8/34 M2, M1 genes for matrix protein 2, matrix protein 1, complete cds
# >LC662542.1 Influenza A virus (H1N1) A/PR/8/34 NA gene for neuraminidase, complete cds
# >LC662541.1 Influenza A virus (H1N1) A/PR/8/34 NP gene for nucleoprotein, complete cds
# >LC662540.1 Influenza A virus (H1N1) A/PR/8/34 HA gene for haemagglutinin, complete cds
# >LC662539.1 Influenza A virus (H1N1) A/PR/8/34 PA, PA-X genes for polymerase PA, PA-X protein, complete cds
# >LC662538.1 Influenza A virus (H1N1) A/PR/8/34 PB1, PB1-F2 genes for polymerase PB1, PB1-F2 protein, complete cds
# >LC662537.1 Influenza A virus (H1N1) A/PR/8/34 PB2 gene for polymerase PB2, complete cds

    samtools faidx complete_1323429_ncbi.fasta LC662537.1 > H1N1_A-PR-8-34_PB2.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662538.1 > H1N1_A-PR-8-34_PB1.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662539.1 > H1N1_A-PR-8-34_PA.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662540.1 > H1N1_A-PR-8-34_HA.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662541.1 > H1N1_A-PR-8-34_NP.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662542.1 > H1N1_A-PR-8-34_NA.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662543.1 > H1N1_A-PR-8-34_M.fasta
    samtools faidx complete_1323429_ncbi.fasta LC662544.1 > H1N1_A-PR-8-34_NS.fasta

# Human cytomegalovirus AD169   10360

# Influenza A virus (H3N2)  41857

# >LC817411.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 8, complete sequence
# >LC817410.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 7, complete sequence
# >LC817409.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 6, complete sequence
# >LC817408.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 5, complete sequence
# >LC817407.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 4, complete sequence
# >LC817406.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 3, complete sequence
# >LC817405.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 2, complete sequence
# >LC817404.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 1, complete sequence

    samtools faidx complete_41857_ncbi.fasta LC817404.1 > H3N2_A-Fukushima-OR808-2023_PB2.fasta
    samtools faidx complete_41857_ncbi.fasta LC817405.1 > H3N2_A-Fukushima-OR808-2023_PB1.fasta
    samtools faidx complete_41857_ncbi.fasta LC817406.1 > H3N2_A-Fukushima-OR808-2023_PA.fasta
    samtools faidx complete_41857_ncbi.fasta LC817407.1 > H3N2_A-Fukushima-OR808-2023_HA.fasta
    samtools faidx complete_41857_ncbi.fasta LC817408.1 > H3N2_A-Fukushima-OR808-2023_NP.fasta
    samtools faidx complete_41857_ncbi.fasta LC817409.1 > H3N2_A-Fukushima-OR808-2023_NA.fasta
    samtools faidx complete_41857_ncbi.fasta LC817410.1 > H3N2_A-Fukushima-OR808-2023_M.fasta
    samtools faidx complete_41857_ncbi.fasta LC817411.1 > H3N2_A-Fukushima-OR808-2023_NS.fasta

# Monkeypox virus   10244: >OP689666.1 Monkeypox virus isolate MPXV/Germany/2022/RKI513, complete genome
    samtools faidx complete_10244_ncbi.fasta OP689666.1 > Monkeypox_isolate_MPXV-Germany-2022-RKI513.fasta

# Human immunodeficiency virus 1    11676: >AJ866558.1 Human immunodeficiency virus 1 complete genome, isolate 01IC-PCI127
    samtools faidx complete_11676_ncbi.fasta AJ866558.1 >  HIV-1_isolate_01IC-PCI127.fasta

# -- Selected genomes saved in the fasta-files --
# Enterovirus_D68_isolate_SH2024-25870.fasta (7391 nt)
# HSV-1_isolate_MacIntyre.fasta (151817 nt)
# HSV-2_strain_G.fasta (155498 nt)
# H1N1_A-PR-8-34_PB2.fasta (2341 nt)
# H1N1_A-PR-8-34_PB1.fasta (2341 nt)
# H1N1_A-PR-8-34_PA.fasta (2233 nt)
# H1N1_A-PR-8-34_HA.fasta (1775 nt)
# H1N1_A-PR-8-34_NP.fasta (1565 nt)
# H1N1_A-PR-8-34_NA.fasta (1413 nt)
# H1N1_A-PR-8-34_M.fasta (1027 nt)
# H1N1_A-PR-8-34_NS.fasta (890 nt)
# Human_cytomegalovirus_strain_AD169.fasta (229354 nt)
# H3N2_A-Fukushima-OR808-2023_PB2.fasta (2301 nt)
# H3N2_A-Fukushima-OR808-2023_PB1.fasta (2316 nt)
# H3N2_A-Fukushima-OR808-2023_PA.fasta (2208 nt)
# H3N2_A-Fukushima-OR808-2023_HA.fasta (1722 nt)
# H3N2_A-Fukushima-OR808-2023_NP.fasta (1536 nt)
# H3N2_A-Fukushima-OR808-2023_NA.fasta (1440 nt)
# H3N2_A-Fukushima-OR808-2023_M.fasta (1002 nt)
# H3N2_A-Fukushima-OR808-2023_NS.fasta (865 nt)
# Monkeypox_isolate_MPXV-Germany-2022-RKI513.fasta (197140 nt)
# HIV-1_isolate_01IC-PCI127.fasta (9752 nt)

(Optional) Run the first round of vrap (–virus==viruses_selected.fasta)

ln -s ~/Tools/vrap/ .
mamba activate /home/jhuang/miniconda3/envs/vrap

cd ~/DATA/Data_Damian/vrap_Ringversuch
cat complete_10244_ncbi.fasta complete_10298_ncbi.fasta complete_10310_ncbi.fasta complete_1323429_ncbi.fasta complete_10360_ncbi.fasta complete_41857_ncbi.fasta complete_10244_ncbi.fasta complete_11676_ncbi.fasta > viruses_selected.fasta

#Run vrap (first round): replace --virus to the specific taxonomy (e.g. viruses_selected.fasta) --> change virus_user_db --> specific_bacteria_user_db
(vrap) for sample in RV1_DNA RV2_DNA RV3_DNA RV4_DNA RV5_DNA RV6_DNA  RV1_RNA RV2_RNA RV3_RNA RV4_RNA RV5_RNA RV6_RNA; do
    vrap/vrap.py  -1 ${sample}_R1.fastq.gz -2 ${sample}_R2.fastq.gz  -o vrap_${sample} --bt2idx=/home/jhuang/REFs/genome --host=/home/jhuang/REFs/genome.fa --virus=/home/jhuang/DATA/Data_Damian/vrap_Ringversuch/viruses_selected.fasta --nt=/mnt/nvme1n1p1/blast/nt --nr=/mnt/nvme1n1p1/blast/nr  -t 100 -l 200  -g
done

Run the second round of vrap (–host==${virus}.fasta)

cat Enterovirus_D68_isolate_SH2024-25870.fasta HSV-1_isolate_MacIntyre.fasta HSV-2_strain_G.fasta H1N1_A-PR-8-34_PB2.fasta H1N1_A-PR-8-34_PB1.fasta H1N1_A-PR-8-34_PA.fasta H1N1_A-PR-8-34_HA.fasta H1N1_A-PR-8-34_NP.fasta H1N1_A-PR-8-34_NA.fasta H1N1_A-PR-8-34_M.fasta H1N1_A-PR-8-34_NS.fasta Human_cytomegalovirus_strain_AD169.fasta H3N2_A-Fukushima-OR808-2023_PB2.fasta H3N2_A-Fukushima-OR808-2023_PB1.fasta H3N2_A-Fukushima-OR808-2023_PA.fasta H3N2_A-Fukushima-OR808-2023_HA.fasta H3N2_A-Fukushima-OR808-2023_NP.fasta H3N2_A-Fukushima-OR808-2023_NA.fasta H3N2_A-Fukushima-OR808-2023_M.fasta H3N2_A-Fukushima-OR808-2023_NS.fasta Monkeypox_isolate_MPXV-Germany-2022-RKI513.fasta HIV-1_isolate_01IC-PCI127.fasta > viruses_representative.fasta

# Run vrap (second round): selecte some representative viruses from the generated Excel-files generated by the last step as --host
(vrap) for virus in Enterovirus_D68_isolate_SH2024-25870 HSV-1_isolate_MacIntyre HSV-2_strain_G H1N1_A-PR-8-34_PB2 H1N1_A-PR-8-34_PB1 H1N1_A-PR-8-34_PA H1N1_A-PR-8-34_HA H1N1_A-PR-8-34_NP H1N1_A-PR-8-34_NA H1N1_A-PR-8-34_M H1N1_A-PR-8-34_NS Human_cytomegalovirus_strain_AD169 H3N2_A-Fukushima-OR808-2023_PB2 H3N2_A-Fukushima-OR808-2023_PB1 H3N2_A-Fukushima-OR808-2023_PA H3N2_A-Fukushima-OR808-2023_HA H3N2_A-Fukushima-OR808-2023_NP H3N2_A-Fukushima-OR808-2023_NA H3N2_A-Fukushima-OR808-2023_M H3N2_A-Fukushima-OR808-2023_NS Monkeypox_isolate_MPXV-Germany-2022-RKI513 HIV-1_isolate_01IC-PCI127; do
    for sample in RV1_DNA RV2_DNA RV3_DNA RV4_DNA RV5_DNA RV6_DNA  RV1_RNA RV2_RNA RV3_RNA RV4_RNA RV5_RNA RV6_RNA; do
        vrap/vrap_until_bowtie2.py  -1 ${sample}_R1.fastq.gz -2 ${sample}_R2.fastq.gz  -o vrap_${sample}_on_${virus} --host /home/jhuang/DATA/Data_Damian/vrap_Ringversuch/${virus}.fasta   -t 100 -l 200  --gbt2 --noblast
    done
done

Generate the mapping statistics for the sam-files generated from last step
```
#Enterovirus_D68_isolate_SH2024-25870
#for virus in HSV-1_isolate_MacIntyre HSV-2_strain_G H1N1_A-PR-8-34_PB2 H1N1_A-PR-8-34_PB1 H1N1_A-PR-8-34_PA H1N1_A-PR-8-34_HA H1N1_A-PR-8-34_NP H1N1_A-PR-8-34_NA H1N1_A-PR-8-34_M H1N1_A-PR-8-34_NS Human_cytomegalovirus_strain_AD169; do
for virus in H3N2_A-Fukushima-OR808-2023_PB2 H3N2_A-Fukushima-OR808-2023_PB1 H3N2_A-Fukushima-OR808-2023_PA H3N2_A-Fukushima-OR808-2023_HA H3N2_A-Fukushima-OR808-2023_NP H3N2_A-Fukushima-OR808-2023_NA H3N2_A-Fukushima-OR808-2023_M H3N2_A-Fukushima-OR808-2023_NS Monkeypox_isolate_MPXV-Germany-2022-RKI513 HIV-1_isolate_01IC-PCI127; do
    for sample in RV1_DNA RV2_DNA RV3_DNA RV4_DNA RV5_DNA RV6_DNA  RV1_RNA RV2_RNA RV3_RNA RV4_RNA RV5_RNA RV6_RNA; do
        echo "-----${sample}_on_${virus}------" >> LOG_mapping
        cd vrap_${sample}_on_${virus}/bowtie
        # Rename and convert SAM to BAM
        mv mapped mapped.sam 2>> ../../LOG_mapping
        samtools view -S -b mapped.sam > mapped.bam 2>> ../../LOG_mapping
        samtools sort mapped.bam -o mapped_sorted.bam 2>> ../../LOG_mapping
        samtools index mapped_sorted.bam 2>> ../../LOG_mapping
        # Write flagstat output to log (go up two levels to write correctly)
        samtools flagstat mapped_sorted.bam >> ../../LOG_mapping 2>&1
        cd ../..
    done
done

#draw some plots for some representative isolates which found in the first round (see Excel-file).
samtools depth -m 0 -a mapped_sorted.bam > coverage.txt
grep "PQ895337.1" coverage.txt > PQ895337_coverage.txt

        import pandas as pd
        import matplotlib.pyplot as plt
        import sys
        import os
        import re

        # Check for required arguments
        if len(sys.argv) != 3:
            print("Usage: python script.py 
```
“) sys.exit(1) # Parse arguments coverage_file = sys.argv[1] genome_length = int(sys.argv[2]) # Extract accession from file name (e.g., “PQ895337” from “PQ895337_coverage.txt”) file_name = os.path.basename(coverage_file) accession_match = re.match(r”([A-Z0-9]+)_coverage\.txt”, file_name) accession = accession_match.group(1) if accession_match else “” # Extract sample name from the grandparent directory of the file sample_dir = os.path.basename(os.path.dirname(os.path.dirname(coverage_file))) sample_name = re.sub(r’^vrap_’, ”, sample_dir).replace(‘_’, ‘ ‘) # Create title and filename plot_title = f”{sample_name} ({accession})” output_filename = plot_title.replace(” “, “_”) + “.png” # Load coverage data df = pd.read_csv( coverage_file, sep=”\t”, header=None, names=[“chr”, “pos”, “coverage”] ) # Create a full genome position index full_index = pd.DataFrame({‘pos’: range(1, genome_length + 1)}) # Merge coverage data with full index df_full = pd.merge(full_index, df[[‘pos’, ‘coverage’]], on=’pos’, how=’left’) df_full[‘coverage’].fillna(0, inplace=True) # Plot plt.figure(figsize=(10, 4)) plt.plot(df_full[“pos”], df_full[“coverage”], color=”blue”, linewidth=0.5) plt.xlabel(“Genomic Position”) plt.ylabel(“Coverage Depth”) plt.title(plot_title) plt.tight_layout() # Save plot to file plt.savefig(output_filename, dpi=150) print(f”Plot saved to {output_filename}”) # Optionally show the plot # plt.show()
Report

Subject: Mapping Results and Selected Reference Genomes

Dear XXXX,

Please find below the results of the mapping analysis. For each virus you provided, I have selected a representative reference isolate, listed as follows:

Selected Reference Isolates

    Enterovirus D68
    • PQ895337.1 – Enterovirus D68 isolate SH2024-25870

    HSV-1 (Herpes Simplex Virus 1)
    • PQ569920.1 – Human alphaherpesvirus 1 isolate MacIntyre, complete genome

    HSV-2 (Herpes Simplex Virus 2)
    • OM370995.1 – Human alphaherpesvirus 2 strain G, complete genome

    Influenza A Virus (H1N1)
    • LC662537.1 – PB2 gene, complete CDS
    • LC662538.1 – PB1 and PB1-F2 genes, complete CDS
    • LC662539.1 – PA and PA-X genes, complete CDS
    • LC662540.1 – HA gene, complete CDS
    • LC662541.1 – NP gene, complete CDS
    • LC662542.1 – NA gene, complete CDS
    • LC662543.1 – M1 and M2 genes, complete CDS
    • LC662544.1 – NS1 and NEP genes, complete CDS

    Cytomegalovirus (strain AD169)
    • X17403.1 – Human cytomegalovirus strain AD169, complete genome

    Influenza A Virus (H3N2)
    • LC817404.1 – PB2 gene
    • LC817405.1 – PB1 genes
    • LC817406.1 – PA genes
    • LC817407.1 – HA gene
    • LC817408.1 – NP gene
    • LC817409.1 – NA gene
    • LC817410.1 – M genes
    • LC817411.1 – NS genes

    Monkeypox Virus
    • OP689666.1 – Isolate MPXV/Germany/2022/RKI513, complete genome

    Human Immunodeficiency Virus 1 (HIV-1)
    • AJ866558.1 – Isolate 01IC-PCI127, complete genome

Mapping Results

    We mapped paired-end reads from 12 Ringversuch project samples against the selected reference genomes.

    Below are the mapping statistics for Enterovirus D68, HSV-1, HSV-2, and H1N1. Coverage plots are attached for all cases where the percentage of reads mapping to the reference genome is greater than 0.00%. Results for the remaining viruses will follow next week.

    (* An asterisk indicates cases with non-zero mapping percentages.)

Mapping Statistics

    Enterovirus D68 (SH2024-25870):

    RV1_DNA: 0 (0.00%)
    RV2_DNA: 0 (0.00%)
    RV3_DNA: 0 (0.00%)
    RV4_DNA: 0 (0.00%)
    RV5_DNA: 0 (0.00%)
    RV6_DNA: 0 (0.00%)
    RV1_RNA: 66 (0.00%)
    RV2_RNA: 55 (0.00%)
    RV3_RNA: 15 (0.00%)
    RV4_RNA: 1701 (0.02%) *
    RV5_RNA: 26 (0.00%)
    RV6_RNA: 35 (0.00%)

    HSV-1 (isolate MacIntyre):

    RV1_DNA: 387 (0.02%) *
    RV2_DNA: 6232 (0.26%) *
    RV3_DNA: 0 (0.00%)
    RV4_DNA: 1443 (0.03%) *
    RV5_DNA: 2 (0.00%)
    RV6_DNA: 0 (0.00%)
    RV1_RNA: 6 (0.00%)
    RV2_RNA: 32 (0.00%)
    RV3_RNA: 4 (0.00%)
    RV4_RNA: 13 (0.00%)
    RV5_RNA: 4 (0.00%)
    RV6_RNA: 10 (0.00%)

    HSV-2 (strain G):

    RV1_DNA: 201 (0.01%) *
    RV2_DNA: 376 (0.02%) *
    RV3_DNA: 0 (0.00%)
    RV4_DNA: 19670 (0.46%) *
    RV5_DNA: 0 (0.00%)
    RV6_DNA: 0 (0.00%)
    RV1_RNA: 0 (0.00%)
    RV2_RNA: 3 (0.00%)
    RV3_RNA: 0 (0.00%)
    RV4_RNA: 25 (0.00%)
    RV5_RNA: 5 (0.00%)
    RV6_RNA: 24 (0.00%)

    Influenza A Virus (H1N1, A/PR/8/34):

    RV1_DNA: 0 (0.00%)
    RV2_DNA: 0 (0.00%)
    RV3_DNA: 0 (0.00%)
    RV4_DNA: 0 (0.00%)
    RV5_DNA: 0 (0.00%)
    RV6_DNA: 0 (0.00%)
    RV1_RNA: 0 (0.00%)
    RV2_RNA: 0 (0.00%)
    RV3_RNA: 0 (0.00%)
    RV4_RNA: 13 + 354 (0.00%)
    RV5_RNA: 0 (0.00%)
    RV6_RNA: 0 (0.00%)

Microbial bioinformatics

Microbial bioinformatics uses computational tools to analyze genomes, track evolution, and study functions in microorganisms, including bacteria and viruses.

Mapping of reads to selected viruses in DAMIAN results (version 2)

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