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Published February 15, 2023 | Version v1
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Supplementary Materials for: Discovery of a novel merbecovirus clone contaminating agricultural rice sequencing datasets from Wuhan, China

  • 1. Independent
  • 2. Department of Biology, University of Puerto Rico - Rio Piedras, San Juan, PR 00931, USA
  • 3. Youthereum Genetics Inc., Toronto, Ontario, Canada
  • 4. Department of Chemistry and Physics, Halmos College of Arts and Sciences, Nova Southeastern University. Ft. Lauderdale, FL, USA
  • 5. Atossa Therapeutics, Inc., Seattle, WA 98104 USA

Description

Supplementary Materials 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

 

Supplementary Information

Supp_Info_1.xlsx: BioProject PRJNA602160 SRA analysis.

Supp_Info_2.xlsx: Mitochondrial sequence analysis for all SRA datasets in BioProject PRJNA602160.

Supp_Info_3.xlsx: MERS-CoV sequence analysis from SRA datasets in BioProject PRJNA602160.

Supp_Infor_4.xlsx: Analysis results for control datasets in PRJNA602115.

Supplementary Data

Snapgene annotated image of HKU4r-HZAU-2020 clone:

SRR10915173_megahit_default_fastp_HKU4r-CoV_IC_k141_13283_del_149bp_Map.png

HKU4r-HZAU-2020 complete sequence in fasta format: HKU4r-HZAU_2020_SRR10915173_k141_13283_del_149.fa

HKU4r-HZAU-2020 annotated full clone in GenBank format: SRR10915173_megahit_default_fastp_HKU4r-CoV_IC_k141_13283_del_149bp.gbk

HKU4r-HZAU-2020 genome only without synthetic vectors in fasta format: HKU4r-HZAU-2020_complete_genome_only.fa

HKU4r-HZAU-2020 annotated genome only in GenBank format: SRR10915173_megahit_default_fastp_HKU4r-CoV_IC_k141_13283_del_149bp_genome_only.gbk

Contigs with high identity to the MERS-CoV genome (NC_019843.3) assembled from pooled SRAs SRR10915167, SRR10915168, SRR10915173, SRR10915174 in fasta format: MEGAHIT_MERS_NC_19843.3_spike_contigs.fa.

Three-dimensional model of the RBD of the HKU4r-HZAU-2020 clone: HKU4r-HZAU-2020_RBD.pdb

Reads in SRR10915167-8 and SRR10915173-4 mapping to the HKU4r-HZAU-2020 clone using minimap2:

SRR10915167-68_73-74_k141_13283_rc_del_149_minimap2_samclip_25.bam

CoronaSPAdes default de novo assembled contigs aligned to the HKU4r-HZAU-2020 clone using minimap2:

SRR10915173_coronaspades_default_k141_13283_rc_del_149_minimap2.bam

SPAdes careful de novo assembled contigs aligned to the HKU4r-HZAU-2020 clone using minimap2:

SRR10915173_spades_careful_k141_13283_rc_del_149_minimap2.bam

metaxa2 rRNA sequences de novo assembled using MEGAHIT:

metaxa2_contigs.zip

Reads from pooled datasets SRR10915167-8 and SRR10915173-4 aligned to S gene section of MERS-CoV genome (NC_019843.3):

SRR10915167-68_73-74_NC_019843_3_S_gene_minimap2.sam

Reads mapping to MERS-CoV (NC_019843.3) S gene and crossing it’s 5’ and 3’ ends showing S gene insertion into HKU4r-HZAU-2020 backbone:

NC_19843.3_spike_gene_3prime_read_stats.txt

NC_19843.3_spike_gene_5prime_read_stats.txt

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