Scoping W-ASAP v2 – RSV

[gordonkoehn]

We're expanding W-ASAP to support RSV surveillance as the next pathogen after SARS-CoV-2. This requires adapting the frontend to handle RSV's dual-backbone structure (RSV-A and RSV-B), which presents our first multi-backbone challenge before tackling the more complex Influenza segmentation.

Key Differences from SARS-CoV-2

Features to retain:

• Variant Explorer (with definitions von GenSpectrum)
• Manual Search

Features to remove:

• Resistance Mutations (not relevant - first RSV vaccine only recently developed, no known resistance)
• Untracked Mutations (variants are currently not quantified in the wastewater - there is no list of known to be present variants)

New challenges:

• Multiple backbones: RSV has two distinct backbones (RSV-A, RSV-B), each requiring separate LAPIS-SILO instances
• This is a stepping stone to Influenza, which will have 4 segments (H1, N1, H3, N2)

Design Decision: Multi-backbone UI Organization

Two approaches to consider:

1. GenSpectrum paradigm: Separate panes/pages per backbone

   • RSV-A: https://genspectrum.org/rsv-a/sequencing-efforts
   • RSV-B: https://genspectrum.org/rsv-b/sequencing-efforts
   • Legacy combined view: https://genspectrum.org/swiss-wastewater/rsv (shows both simultaneously)

2. Unified selection: Single "RSV" entry with subtype selector

   • Could reduce navigation complexity
   • May be more complex to implement

Trade-offs:

• Organization vs. implementation complexity
• Consider Influenza preview: https://genspectrum.org/swiss-wastewater/flu (4 segments displayed together)
• Notable variants/lineages are defined per segment in practice – so each could be considered its own virus

Decision needed: How do we want to handle multi-backbone display in the UI?

Below some of the initials todo's I envision:

Initial Implementation Tasks

Phase 0: Planning

• Schedule meeting with @AugusteRi to understand Influenza requirements
  • Understand variant definition patterns per segment
  • Identify UI/UX patterns that scale from 2 backbones (RSV) to 4 segments (Influenza)

Phase 1: RSV-A Staging Instance

• Refactor COVID frontend to be reusable
• Make analysis modes configurable, so we can have only manual and variant
• Setup staging page for RSV-A
• @gordonkoehn: Setup testing LAPIS-SILO instance for RSV
• Swap API from COVID to RSV-A

[gordonkoehn]

• same reference as on NextStrain / GenSpectrum
• No Resistance Mutations
• RSV A und B separate viruses // A first.
• Linkouts per Mutation to GenSpectrum e.g. for F:S337N to here

[gordonkoehn]

The SIB just released som resistance mutation sets we could use here now, see Viralzone, or in particular the file for RSV-A and B