wastewaterConfig.ts

import type { MutationAnnotation } from '@genspectrum/dashboard-components/util';

import type { ResistanceMutationCollectionConfig } from '../components/views/wasap/wasapPageConfig';
import { VARIANT_TIME_FRAME, type WasapPageConfig } from '../components/views/wasap/wasapPageConfig';

export const wastewaterOrganisms = {
    covid: 'covid',
    rsvA: 'rsv-a',
    rsvB: 'rsv-b',
} as const;

export type WastewaterOrganismName = (typeof wastewaterOrganisms)[keyof typeof wastewaterOrganisms];

export const wastewaterPathFragment = 'swiss-wastewater';

export const wastewaterOrganismConfigs: Record<WastewaterOrganismName, WasapPageConfig> = {
    [wastewaterOrganisms.covid]: {
        internalName: wastewaterOrganisms.covid,
        name: 'SARS-CoV-2',
        path: `/${wastewaterPathFragment}/covid`,
        description: 'Analyze SARS-CoV-2 data that was collected by the WISE project.',
        linkTemplate: {
            nucleotideMutation:
                'https://open.cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?nucMutations={{mutation}}',
            aminoAcidMutation:
                'https://open.cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?aaMutations={{mutation}}',
        },
        manualAnalysisModeEnabled: true,
        variantAnalysisModeEnabled: true,
        resistanceAnalysisModeEnabled: true,
        untrackedAnalysisModeEnabled: true,
        collectionAnalysisModeEnabled: true,
        defaultAnalysisMode: 'resistance',
        resistanceMutationCollections: [
            {
                collectionId: 4,
                name: '3CLpro',
                annotationSymbol: 'c',
                description:
                    'SARS-CoV-2 3C-like protease (3CLpro, or Mpro for Main protease) inhibitor resistance mutation as per <a class="link" href="https://covdb.stanford.edu/drms">Stanford Coronavirus Antiviral & Resistance database</a> (last updated on 21 August 2024).',
            },
            {
                collectionId: 5,
                name: 'RdRp',
                annotationSymbol: 'r',
                description:
                    'SARS-CoV-2 RNA-dependent RNA polymerase (RdRP) inhibitor resistance mutation as per <a class="link" href="https://covdb.stanford.edu/drms">Stanford Coronavirus Antiviral & Resistance database</a> (last updated on 21 August 2024).',
            },
            {
                collectionId: 6,
                name: 'Spike',
                annotationSymbol: 's',
                description:
                    'SARS-CoV-2 Spike monoclonal antibody (mAb) resistance mutation as per <a class="link" href="https://covdb.stanford.edu/drms">Stanford Coronavirus Antiviral & Resistance database</a> (last updated on 21 August 2024).',
            },
        ] satisfies ResistanceMutationCollectionConfig[],
        lapisBaseUrl: 'https://lapis.wasap.genspectrum.org/covid',
        samplingDateField: 'samplingDate',
        locationNameField: 'locationName',
        predefinedVariantsSource: {
            collectionsUserId: 3,
            collectionsTag: '#pango-lineage',
            variantSourceLabel: 'Nextclade',
        },
        clinicalLapis: {
            lapisBaseUrl: 'https://lapis.cov-spectrum.org/open/v2',
            dateField: 'date',
            cladeField: 'nextstrainClade',
            lineageField: 'nextcladePangoLineage',
        },
        browseDataUrl: 'https://db.wasap.genspectrum.org/covid/search',
        browseDataDescription: 'Browse the data in the W-ASAP Loculus instance.',
        collectionsApiBaseUrl: 'https://cov-spectrum.org/api/v2',
        collectionTitleFilter: 'wastewater',
        defaultLocationName: 'Zürich (ZH)',
        clinicalSequenceCountWarningThreshold: 50,
        filterDefaults: {
            manual: {
                mode: 'manual',
                sequenceType: 'nucleotide',
                mutations: undefined,
            },
            variant: {
                mode: 'variant',
                signatureType: 'computed',
                sequenceType: 'nucleotide',
                variant: 'XFG*',
                minProportion: 0.8,
                minCount: 15,
                minJaccard: 0.75,
                timeFrame: VARIANT_TIME_FRAME.all,
                collectionId: 4961,
            },
            resistance: {
                mode: 'resistance',
                sequenceType: 'amino acid',
                resistanceSet: 'Spike',
            },
            untracked: {
                mode: 'untracked',
                sequenceType: 'nucleotide',
                excludeSet: 'predefined',
            },
            collection: {
                mode: 'collection',
                collectionId: 1,
            },
        },
    },
    [wastewaterOrganisms.rsvA]: {
        internalName: wastewaterOrganisms.rsvA,
        name: 'RSV-A',
        path: `/${wastewaterPathFragment}/rsv-a`,
        description: 'Analyze RSV-A data that was collected by the WISE project.',
        linkTemplate: {
            nucleotideMutation:
                'https://genspectrum.org/rsv-a/single-variant?sampleCollectionDateRangeLower=Last+year&nucleotideMutations={{mutation}}',
            aminoAcidMutation:
                'https://genspectrum.org/rsv-a/single-variant?sampleCollectionDateRangeLower=Last+year&aminoAcidMutations={{mutation}}',
        },
        manualAnalysisModeEnabled: true,
        variantAnalysisModeEnabled: true,
        lapisBaseUrl: 'https://lapis.wasap.genspectrum.org/rsva',
        samplingDateField: 'samplingDate',
        locationNameField: 'locationName',
        clinicalLapis: {
            lapisBaseUrl: 'https://lapis.pathoplexus.org/rsv-a',
            dateField: 'sampleCollectionDateRangeLower',
            lineageField: 'lineage',
        },
        browseDataUrl: 'https://db.wasap.genspectrum.org/rsva/search',
        browseDataDescription: 'Browse the data in the W-ASAP Loculus instance.',
        defaultLocationName: 'Geneva',
        clinicalSequenceCountWarningThreshold: 50,
        filterDefaults: {
            manual: {
                mode: 'manual',
                sequenceType: 'nucleotide',
                mutations: undefined,
            },
            variant: {
                mode: 'variant',
                signatureType: 'computed',
                sequenceType: 'nucleotide',
                variant: 'A.D.1*',
                minProportion: 0.8,
                minCount: 15,
                minJaccard: 0.75,
                timeFrame: VARIANT_TIME_FRAME.all,
            },
        },
    },
    [wastewaterOrganisms.rsvB]: {
        internalName: wastewaterOrganisms.rsvB,
        name: 'RSV-B',
        path: `/${wastewaterPathFragment}/rsv-b`,
        description: 'Analyze RSV-B data that was collected by the WISE project.',
        linkTemplate: {
            nucleotideMutation:
                'https://genspectrum.org/rsv-b/single-variant?sampleCollectionDateRangeLower=Last+year&nucleotideMutations={{mutation}}',
            aminoAcidMutation:
                'https://genspectrum.org/rsv-b/single-variant?sampleCollectionDateRangeLower=Last+year&aminoAcidMutations={{mutation}}',
        },
        manualAnalysisModeEnabled: true,
        variantAnalysisModeEnabled: true,
        lapisBaseUrl: 'https://lapis.wasap.genspectrum.org/rsvb',
        samplingDateField: 'samplingDate',
        locationNameField: 'locationName',
        clinicalLapis: {
            lapisBaseUrl: 'https://lapis.pathoplexus.org/rsv-b',
            dateField: 'sampleCollectionDateRangeLower',
            lineageField: 'lineage',
        },
        browseDataUrl: 'https://db.wasap.genspectrum.org/rsvb/search',
        browseDataDescription: 'Browse the data in the W-ASAP Loculus instance.',
        defaultLocationName: 'Zurich',
        clinicalSequenceCountWarningThreshold: 50,
        filterDefaults: {
            manual: {
                mode: 'manual',
                sequenceType: 'nucleotide',
                mutations: undefined,
            },
            variant: {
                mode: 'variant',
                signatureType: 'computed',
                sequenceType: 'nucleotide',
                variant: 'B.D.E.1*',
                minProportion: 0.8,
                minCount: 15,
                minJaccard: 0.75,
                timeFrame: VARIANT_TIME_FRAME.all,
            },
        },
    },
};

function withResistanceCollectionOverrides(config: WasapPageConfig): WasapPageConfig {
    // eslint-disable-next-line @typescript-eslint/naming-convention
    const stagingIds: Record<string, number> = { '3CLpro': 4, 'RdRp': 5, 'Spike': 6 };
    return {
        ...config,
        ...(config.resistanceAnalysisModeEnabled && {
            resistanceMutationCollections: config.resistanceMutationCollections.map((set) => ({
                ...set,
                collectionId: stagingIds[set.name] ?? set.collectionId,
            })),
        }),
        ...(config.variantAnalysisModeEnabled &&
            config.predefinedVariantsSource !== undefined && {
                predefinedVariantsSource: {
                    ...config.predefinedVariantsSource,
                    collectionsUserId: 1,
                },
            }),
    };
}

export const wastewaterOrganismStagingConfigs: Record<WastewaterOrganismName, WasapPageConfig> = {
    ...wastewaterOrganismConfigs,
    [wastewaterOrganisms.covid]: withResistanceCollectionOverrides(
        wastewaterOrganismConfigs[wastewaterOrganisms.covid],
    ),
};

export const wastewaterConfig = {
    menuListEntryDecoration: 'decoration-teal',
    backgroundColor: 'bg-tealMuted',
    backgroundColorFocus: 'group-hover:bg-teal',
    borderEntryDecoration: 'hover:border-teal',
    browseDataUrl: 'https://wise-loculus.genspectrum.org',
    browseDataDescription: 'Browse the data in the WISE Loculus instance.',
    lapisBaseUrl: 'https://api.wise-loculus.genspectrum.org',
    pages: {
        rsv: {
            path: `/${wastewaterPathFragment}/rsv`,
            description: 'Analyze RSV data that was collected by the WISE project.',
        },
        influenza: {
            path: `/${wastewaterPathFragment}/flu`,
            description: 'Analyze Influenza data that was collected by the WISE project.',
        },
    },
};

export const wastewaterBreadcrumb = {
    name: 'Swiss Wastewater',
    href: `/${wastewaterPathFragment}`,
};

export const RSVTypes = ['RSV-A', 'RSV-B'] as const;

export type RSVType = (typeof RSVTypes)[number];

export const InfluenzaTypes = ['H1', 'N1', 'H3', 'N2'] as const;

export type InfluenzaType = (typeof InfluenzaTypes)[number];

export function getMutationAnnotation(reference: InfluenzaType): MutationAnnotation[] {
    switch (reference) {
        case 'N1':
            return mutationAnnotationsN1;
        case 'N2':
            return mutationAnnotationsN2;
        default:
            return [];
    }
}

function symbolMap(medication: string): string {
    switch (medication) {
        case 'Laninamivir':
            return '*';
        case 'Oseltamivir':
            return '!';
        case 'Peramivir':
            return '^';
        case 'Zanamivir':
            return '+';
        default:
            return '';
    }
}

function createMutationAnnotation(medication: string, aaMutationList: string[]): MutationAnnotation {
    return {
        name: `${medication} resistance mutations`,
        description: `This mutation is associated with reduced inhibition by ${medication}, for more details see the <a class='link' href='https://www.who.int/teams/global-influenza-programme/laboratory-network/quality-assurance/antiviral-susceptibility-influenza/neuraminidase-inhibitor'>Global Influenza Programme Report</a>.`,
        symbol: symbolMap(medication),
        nucleotideMutations: [],
        aminoAcidMutations: aaMutationList,
    };
}

// See https://github.com/anna-parker/NAIMutations/tree/main for calculation details
// TODO(#650): Some mutations are only of interest when with other mutations (e.g. deletions) but are now marked individually
const mutationAnnotationsN1: MutationAnnotation[] = [
    createMutationAnnotation('Laninamivir', [
        'P458T',
        'S247R',
        'H275Y',
        'E119A',
        'Q136K',
        'E119D',
        'E119G',
        'Q136R',
        'I223R',
        'I427T',
        'I223K',
        'I436N',
        'R152K',
    ]),
    createMutationAnnotation('Oseltamivir', [
        'E119D',
        'I223R',
        'I427T',
        'E119V',
        'S247N',
        'P458T',
        'I223M',
        'S247G',
        'R293K',
        'I223L',
        'S247R',
        'Q313R',
        'N295S',
        'I223K',
        'R152K',
        'D199E',
        'H275Y',
        'D199N',
        'E119A',
        'D199Y',
        'G147R',
        'E119G',
        'I223V',
        'I436N',
        'D199G',
    ]),
    createMutationAnnotation('Peramivir', [
        'P458T',
        'S247R',
        'H275Y',
        'Q136K',
        'D199N',
        'G147R',
        'E119D',
        'E119G',
        'Q136R',
        'I223R',
        'I223K',
        'E119V',
        'I436N',
        'I223V',
        'S247N',
    ]),
    createMutationAnnotation('Zanamivir', [
        'P458T',
        'S247R',
        'H275Y',
        'E119A',
        'Q136K',
        'D199Y',
        'E119D',
        'E119G',
        'S110F',
        'Q136R',
        'I427T',
        'E119V',
        'I436N',
        'I223K',
        'I223R',
        'I117R',
    ]),
];

// WHO uses reference KJ609208.1 and AB124658.1, mutations here use reference CY114383.1
// When KJ609208.1 and AB124658.1 are aligned to CY114383.1 using nextclade we see no insertions/deletions only mutations
// Therefore, we can use CY114383.1 as the reference for the mutations
// See https://github.com/anna-parker/NAIMutations/tree/main for calculation details
// TODO(#650): Some mutations are only of interest when with other mutations (e.g. deletions) but are now marked individually
const mutationAnnotationsN2: MutationAnnotation[] = [
    createMutationAnnotation('Laninamivir', ['T148I', 'E119V', 'N142S']),
    createMutationAnnotation('Oseltamivir', [
        'E276D',
        'N329R',
        'N245Y',
        'E119V',
        'K249E',
        'R371K',
        'R292K',
        'S331R',
        'T148I',
        'E119I',
        'I222V',
        'N294S',
        'D151E',
        'I222L',
        'I222T',
        'R224K',
        '247-',
        'Q391K',
        'N142S',
        '248-',
        '245-',
        '250-',
    ]),
    createMutationAnnotation('Peramivir', ['N142S', 'E119V', 'R292K', 'D151A', 'T148I']),
    createMutationAnnotation('Zanamivir', [
        'E276D',
        'R224K',
        'E119I',
        'Q136K',
        '247-',
        'Q391K',
        'E119D',
        'R371K',
        'N142S',
        'K249E',
        'E119V',
        'R292K',
        '250-',
        'D151G',
        'D151A',
        'T148I',
    ]),
];