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.
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 |
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 |
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 |
Andersen Lab
The Scripps Research Institute
La Jolla, CA, USA
data@andersen-lab.com