As linked in this new GitHub Issue, we’re wondering if there are users who are performing this kind of surveillance, and if so what kind of targets/parts would need to be added to support this? We’re keen to add functionality for these, but are wanting feedback from users as well. I’m going to do a cursory literature review, but would welcome outside input.
It seems as though there is little consensus still in which markers are being used to detect hantaviruses in wastewater - the same seems to apply to ebolaviruses, which are also an important concern right now. Given that there is some variability in reporting, we have added the different viruses as parts for the upcoming v3.0.1 release, which can be used as measures, and then det or detected can be used as the unit, with a value of TRUE or FALSE.
The upcoming hantavirus and ebolavirus additions:
| partID | partLabel |
|---|---|
| ebolaGrp | Orthoebolavirus Group |
| ebolaV | Ebola virus, Orthoebolavirus zairense |
| sudanV | Sudan virus, Orthoebolavirus sudanense |
| taiforestV | Taï Forest virus, Orthoebolavirus taiense |
| bundibugyoV | Bundibugyo virus, Orthoebolavirus bundibugyoense |
| EVD | Ebola Virus Disease (EVD) |
| hantaGrp | Orthohantavirus Group |
| andv | Andes virus (ANDV) hantavirus |
| snv | Sin Nombre virus (SNV) hantavirus |
| htnv | Hantaan virus (HTNV) hantavirus |
| seov | Seoul virus (SEOV) hantavirus |
| puuv | Puumala virus (PUUV) hantavirus |
| dobv | Dobrava-Belgrade virus (DOBV) hantavirus |
| hfrs | Hantavirus hemorrhagic fever with renal syndrome (HFRS) |
| hps | Hantavirus pulmonary syndrome (HPS) |
Theses include the “group” part types for hantaviruses and ebolaviruses, the specific viruses in each group, and one or more of the disease states caused by the viruses (used for reporting aggregated clinical and population surveillance measures.
For example, if reporting a single positive detection of andes virus (shortened measures table) from cruise ship wastewater:
| Measure Report ID | Sample ID | Site ID | Analysis date start | Compartment | Specimen | Group | Measure | Value | Unit | Aggregation |
|---|---|---|---|---|---|---|---|---|---|---|
| andes_hanta_test1 | ship_1 | cruiseShip | 07-07-2026 | wat | sa | hantaGrp | andv | TRUE | det | sin |