Supplementary Data for: Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China

Supplementary Data for

Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China

Adrian Jones, Daoyu Zhang, Steven E. Massey,  Yuri Deigin, Louis R. Nemzer, Steven C. Quay

Data S1: HKU4r-HZAU-2020 DNA clone complete sequence in fasta file format: S1_HKU4r-HZAU_2020_SRR10915173_k141_13283_del_149.fa.

Data S2: Reads in SRR10915167-8 and SRR10915173-4 mapping to the HKU4r-HZAU-2020 clone using minimap2: S2_SRR10915167-68_73-74_k141_13283_rc_del_149_minimap2_samclip_25.sam.

Data S3: Mapping statistics for reads in Data S2: S3_SRR10915167-68_73-74_k141_13283_rc_del_149_minimap2_samclip_25_stats.txt.

Data S4: Contigs with high identity to the MERS-CoV genome (NC_019843.3) assembled from pooled SRAs SRR10915167, SRR10915168, SRR10915173, SRR10915174 in fasta format: S4_MEGAHIT_MERS_NC_19843.3_spike_contigs.fa.

Data S5: Reads from pooled datasets SRR10915167-8 and SRR10915173-4 aligned to S gene section of MERS-CoV genome (NC_019843.3): S5_SRR10915167-68_73-74_NC_019843_3_S_gene_minimap2.sam.

Data S6: Reads mapping to MERS-CoV (NC_019843.3) S gene and crossing it’s 5’ end showing S gene insertion into HKU4r-HZAU-2020 backbone: S6_NC_19843.3_spike_gene_5prime_read_stats.txt

Data S7: Reads mapping to MERS-CoV (NC_019843.3) S gene and crossing it’s 3’ end showing S gene insertion into HKU4r-HZAU-2020 backbone: S7_NC_19843.3_spike_gene_3prime_read_stats.txt

Data S8: SPAdes careful de novo assembled contigs aligned to the HKU4r-HZAU-2020 clone using minimap2: S8_SRR10915173_spades_careful_k141_13283_rc_del_149_minimap2.sam

Data S9: CoronaSPAdes default de novo assembled contigs aligned to the HKU4r-HZAU-2020 clone using minimap2: S9_SRR10915173_coronaspades_default_k141_13283_rc_del_149_minimap2.sam

Data S10: Three-dimensional model of the RBD of the HKU4r-HZAU-2020 clone: S10_pymol_RBD.pdb

Data S11: HKU4r-HZAU-2020 annotated DNA clone in GenBank file format: S11_SRR10915173_megahit_default_fastp_HKU4r-CoV_IC_k141_13283_del_149bp.gbk 

Data S12: HKU4r-HZAU-2020 annotated genome only (without synthetic vectors) in GenBank format: S12_SRR10915173_megahit_default_fastp_HKU4r-CoV_IC_k141_13283_del_149bp_genome_only.gbk

Data S13: SnapGene annotated image of HKU4r-HZAU-2020 clone: S13_SRR10915173_megahit_default_fastp_HKU4r-CoV_IC_k141_13283_del_149bp_Map.png

Data S14: Metaxa2 rRNA sequences de novo assembled using MEGAHIT for  SRA datasets SRR10915167, SRR10915168, SRR10915173, SRR10915174 in BioProject PRJNA602160: S14_metaxa2_contigs.zip

Data S15: HKU4r-HZAU-2020 genome only (without synthetic vectors) in fasta format: S15_HKU4r-HZAU-2020_complete_genome_only.fa