Improved geo_loc_admin1 for North Macedonian CCHF sequences submitted by Uni of Pecs, based on location in isolate name #1
Description
Describe the possible issue
Geolocation is not as precise as it can be, based on further information from the isolate name.
Evidence of the problem
https://pathoplexus.org/seq/PP_000RFLV.2: Admin 1 is Kriva Palanka, see also -> https://www.ncbi.nlm.nih.gov/nuccore/PQ031236.1, https://www.geonames.org/863869/kriva-palanka.html
https://pathoplexus.org/seq/PP_000RFMT.2 has Admin 1: Arachinovo, https://www.geonames.org/863831/opstina-aracinovo.html
https://pathoplexus.org/seq/PP_000RF4U.2 has Admin 1: Karbinci, City: Kucica, see https://www.geonames.org/788935/kucica.html (also spelled Kuchica) [Patient 1]
All first parts of the isolate names map perfectly to North Macedonian locations.
The oldest sample (Kuchica) is described in two associated publications:
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.34.2300409
Suggested change
| PP accession | Admin 1 | City | Collection Date | Paper URL |
|---|---|---|---|---|
| PP_000RFLV.2 | Kriva Palanka | |||
| PP_000RFMT.2 | Arachinovo | |||
| PP_000RF4U.2 | Karbinci | Kucica | 2023-07 (instead of current 2023) | https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.34.2300409, https://assets-eu.researchsquare.com/files/rs-4360716/v1/21a390d9-967e-402f-bd9f-c9e6ad3eaf8a.pdf?c=1715100422 |
Aside
Two more sequences seem to be from the same outbreak, from different sequencers. In this case, one sequence is labeled as index patient and also Kuchica, matching Patient 1 from above.
The other sequence is labeled Skopje and "infected healthcare worker", matching the description from the papers above. So geolocation and dates could be narrowed for these as well.
https://pathoplexus.org/seq/PP_000RFJZ.2
https://pathoplexus.org/seq/PP_000RFKX.2