Table 3 Iterative Analysis on Non-host Reads of Sample 712, 806, 808, 819, 820, 1500, and 1501. Collected known samples (Table 2) were analyzed using the ECBC iterative analysis pipeline for pathogen detection. De novo assembled contigs are used to generate nearest neighbors, then the nearest neighbors are used to map reads and generate consensus contigs from the mapped reads (Fig. 2). Upon completion, a new iteration begins using reads not mapped to the nearest neighbor. The cycle completes after no further reads exist for contig building or there are no matches reported

712

1

759

3

Lujo virus segment S glycoprotein precursor and nucleocapsid protein genes, complete cds

2

2

90

1

Lujo virus segment L multifunctional matrix-like protein and large RNA-dependent RNA polymerase genes, complete cds

1

806

1

4752

0

-

-

808

1

4479

4

Lujo virus segment L multifunctional matrix-like protein and large RNA-dependent RNA polymerase genes, complete cds

3

2

1527

1

Lujo virus segment S glycoprotein precursor and nucleocapsid protein genes, complete cds

1

3

139

0

-

-

819

1

12450

12

Zaria bat coronavirus strain ZBCoV, partial genome

1

2

8247

9

-

no db hits

820

1

14790

31

Rhinolophus ferrumequinum clone VMRC7-267P18, complete sequence

1

2

10222

37

Zaria bat coronavirus strain ZBCoV, partial genome

1

3

9704

33

-

no db hits

1500

1

884863

3993

Middle East respiratory syndrome coronavirus complete genome

1

2

26795

37

Actinobacillus suis H91-0380 complete genome

1

3

26643

36

Middle East respiratory syndrome coronavirus Isolate Qatar4 complete genome

12

1501

1

828116

3967

Middle East respiratory syndrome coronavirus complete genome

1

2

26937

33

Actinobacillus suis H91-0380 complete genome

17

3

26761

34

PREDICTED: Equus caballus uncharacterized LOC102148405 (LOC102148405)

1