Curated alignments

We periodically combine genomic sequences generated as part of our consortium with publicly available sequences. Our curated alignments do not include:

• laboratory strains (adapted, passaged, recombinant, antiviral & vaccine experiments)

• sequences without a timestamp

• subsequent timepoints, if multiple timepoints are available

• duplicates (when more than one sequence is available for a single strain)

Remaining sequences are trimmed to their coding regions, aligned using mafft and inspected manually. At this step we discard:

• low quality sequences (manual curation)

• incomplete sequences (<95% of (NP+GPC) or (L+Z) or (NP+VP35+VP40+GP+VP30+VP24+L) ORFs length)

ORFs are arranged in sense orientation as follows:

Lassa S segment: NP -NNN- GPC

Lassa L segment: L -NNN- Z

Ebola: NP -NNN- VP35 -NNN- VP40 -NNN- GP -NNN- VP30 -NNN- VP24 -NNN- L

For each alignment, a maximum likelihood (ML) phylogeny is reconstructed with IQ-TREE with ultrafast bootstrap approximation (1000 replicates).

We will be releasing such curated alignments periodically to be used by the broader community for downstream analyses.

Lassa S segment

Alignment File: LASV_NP_GPC_2022.03.18.fasta

Total Number of sequences: 690

FASTA header format:

> GenBank Accession | Species | Outcome | Country | Date

ML Tree file: LASV_NP_GPC_2022.03.18.newick

Key:

Species

Code	Species	Count
Hs	Homo sapiens	625
Hp	Hylomyscus pamfi	1
Me	Mastomys erythroleucus	9
Mn	Mastomys natalensis	53
Unk	Unknown	2

Country

Code	Country	Count
BEN	Benin	11
CIV	Ivory Coast	13
GIN	Guinea	12
LBR	Liberia	25
MLI	Mali	5
NGA	Nigeria	486
SLE	Sierra Leone	136
TGO	Togo	2

Outcome

Code	Outcome	Count
Died	Died	134
Discharged	Discharged	97
Unk	Unknown	459

Lassa L segment

Alignment File: LASV_L_Z_2022.03.18.fasta

Total Number of sequences: 534

FASTA header format:

> GenBank Accession | Species | Outcome | Country | Date

ML Tree file: LASV_L_Z_2022.03.18.newick

Key:

Species

Code	Species	Count
Hs	Homo sapiens	487
Hp	Hylomyscus pamfi	1
Me	Mastomys erythroleucus	9
Mn	Mastomys natalensis	35
Unk	Unknown	2

Country

Code	Country	Count
BEN	Benin	10
CIV	Ivory Coast	13
GIN	Guinea	12
LBR	Liberia	22
MLI	Mali	3
NGA	Nigeria	386
SLE	Sierra Leone	86
TGO	Togo	2

Outcome

Code	Outcome	Count
Died	Died	114
Discharged	Discharged	79
UNK	Unknown	341

Ebola

Alignment File: EBOV_ORFs_2021.11.24.fasta

Total Number of sequences: 2790

FASTA header format:

> GenBank Accession | Species | Outcome | Country | Date

ML Tree file: EBOV_ORFs_2021.11.24.newick

Key:

Species

Code	Species	Count
Hs	Homo sapiens	2790

Country

Code	Country	Count
COD	Democratic Republic of the Congo	801
COG	Republic of the Congo	2
GAB	Gabon	7
GIN	Guinea	354
LBR	Liberia	243
MLI	Mali	4
NGA	Nigeria	11
SLE	Sierra Leone	1362
Unk	Unknown	6
USA	United States	1

Outcome

Code	Outcome	Count
Died	Died	384
Discharged	Discharged	151
Unk	Unknown	2255

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Andersen Lab
The Scripps Research Institute
La Jolla, CA, USA
[email protected]