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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

LASV_NP_GPC_2022.03.18.png

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 LASV_L_Z_2022.03.18.png

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 EBOV_ORFs_2021.11.24.png

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

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

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