diff --git a/src/api/models/indexes/main.go b/src/api/models/indexes/main.go
index 12f94edd..7fb93e97 100644
--- a/src/api/models/indexes/main.go
+++ b/src/api/models/indexes/main.go
@@ -33,14 +33,10 @@ type Sample struct {
 }
 
 type Variation struct {
-	Genotype             Genotype   `json:"genotype"`
-	GenotypeProbability  []float64  `json:"genotypeProbability"`  // -1 = no call (equivalent to a '.')
-	PhredScaleLikelyhood []float64  `json:"phredScaleLikelyhood"` // -1 = no call (equivalent to a '.')
-	Alleles              AllelePair `json:"alleles"`
-}
-type AllelePair struct {
-	Left  string `json:"left"`
-	Right string `json:"right"`
+	Genotype             Genotype  `json:"genotype"`
+	GenotypeProbability  []float64 `json:"genotypeProbability"`  // -1 = no call (equivalent to a '.')
+	PhredScaleLikelyhood []float64 `json:"phredScaleLikelyhood"` // -1 = no call (equivalent to a '.')
+	Alleles              []string  `json:"alleles"`
 }
 
 type Genotype struct {
diff --git a/src/api/mvc/variants/main.go b/src/api/mvc/variants/main.go
index c10e12bf..7713de91 100644
--- a/src/api/mvc/variants/main.go
+++ b/src/api/mvc/variants/main.go
@@ -677,7 +677,7 @@ func executeGetByIds(c echo.Context, ids []string, isVariantIdQuery bool, isDocu
 
 						SampleId:     sampleId,
 						GenotypeType: zygosity.ZygosityToString(variant.Sample.Variation.Genotype.Zygosity),
-						Alleles:      []string{alleles.Left, alleles.Right},
+						Alleles:      alleles,
 
 						AssemblyId: variant.AssemblyId,
 						DocumentId: docId,
diff --git a/src/api/repositories/elasticsearch/variants.go b/src/api/repositories/elasticsearch/variants.go
index 90ebeec9..929aac42 100644
--- a/src/api/repositories/elasticsearch/variants.go
+++ b/src/api/repositories/elasticsearch/variants.go
@@ -658,61 +658,27 @@ func DeleteVariantsByTableId(es *es7.Client, cfg *models.Config, tableId string)
 // -- internal use only --
 
 func addAllelesToShouldMap(alleles []string, genotype c.GenotypeQuery, allelesShouldMap []map[string]interface{}) ([]map[string]interface{}, int) {
-	minimumShouldMatch := 0
-
-	if len(alleles) > 0 {
-		switch len(alleles) {
-		case 1:
-			if genotype == gq.ALTERNATE || genotype == gq.REFERENCE {
-				// haploid case
-
-				// queried allele should be present on the left side of the pair with an empty right side
-				allelesShouldMap = append(allelesShouldMap, map[string]interface{}{
-					"query_string": map[string]interface{}{
-						"query": "sample.variation.alleles.left.keyword:" + alleles[0] + " AND sample.variation.alleles.right.keyword:\"\"",
-					}})
-
-			} else {
-				// assume diploid-type of search as default
-
-				//  queried allele can be present on either side of the pair
-				allelesShouldMap = append(allelesShouldMap, map[string]interface{}{
-					"query_string": map[string]interface{}{
-						"query": "sample.variation.alleles.left.keyword:" + alleles[0] + " OR sample.variation.alleles.right.keyword:" + alleles[0],
-					}})
+	minimumShouldMatch := 1
+
+	queryStrBuild := ""
+	for i, al := range alleles {
+		if i == 0 {
+			queryStrBuild += al
+		} else {
+			switch genotype {
+			case gq.ALTERNATE: // haploid
+			case gq.REFERENCE:
+				queryStrBuild = fmt.Sprintf("%s OR %s", queryStrBuild, al)
+			default: // diploid ++
+				queryStrBuild = fmt.Sprintf("%s AND %s", queryStrBuild, al)
 			}
-		case 2:
-			if genotype == gq.ALTERNATE || genotype == gq.REFERENCE {
-				// haploid case
-
-				// either queried allele can be present on the left side of the pair with an empty right side
-				allelesShouldMap = append(allelesShouldMap, map[string]interface{}{
-					"query_string": map[string]interface{}{
-						"query": "sample.variation.alleles.left.keyword:" + alleles[0] + " AND sample.variation.alleles.right.keyword:\"\"",
-					}})
-				allelesShouldMap = append(allelesShouldMap, map[string]interface{}{
-					"query_string": map[string]interface{}{
-						"query": "sample.variation.alleles.left.keyword:" + alleles[1] + " AND sample.variation.alleles.right.keyword:\"\"",
-					}})
-
-			} else {
-				// assume diploid-type of search as default
-
-				// treat as a left/right pair
-				// either queried allele can be present on the left or right side of the pair
-				allelesShouldMap = append(allelesShouldMap, map[string]interface{}{
-					"query_string": map[string]interface{}{
-						"query": "sample.variation.alleles.left.keyword:" + alleles[0] + " AND sample.variation.alleles.right.keyword:" + alleles[1],
-					}})
-				allelesShouldMap = append(allelesShouldMap, map[string]interface{}{
-					"query_string": map[string]interface{}{
-						"query": "sample.variation.alleles.left.keyword:" + alleles[1] + " AND sample.variation.alleles.right.keyword:" + alleles[0],
-					}})
-			}
-			// TODO: triploid ?
 		}
-		minimumShouldMatch = 1
 	}
+	allelesShouldMap = append(allelesShouldMap, map[string]interface{}{
+		"query_string": map[string]interface{}{
+			"default_field": "sample.variation.alleles",
+			"query":         queryStrBuild,
+		}})
 
 	return allelesShouldMap, minimumShouldMatch
 }
diff --git a/src/api/services/ingestion.go b/src/api/services/ingestion.go
index 07e35551..8296f7d6 100644
--- a/src/api/services/ingestion.go
+++ b/src/api/services/ingestion.go
@@ -746,22 +746,22 @@ func (i *IngestionService) ProcessVcf(
 						// ...  REF		ALT			...
 						// ...  G		CT,CTT,CTTT
 
-						var alleles indexes.AllelePair
+						alleles := make([]string, 0)
 						// hold a temporary pointer to the current state of this-variant's 'alt' and 'ref' for brevity
 						tmpVariantAlt := tmpVariant["alt"].([]string)
 						tmpVariantRef := tmpVariant["ref"].([]string)
 
 						if alleleLeft > 0 {
-							alleles.Left = tmpVariantAlt[alleleLeft-1]
+							alleles = append(alleles, tmpVariantAlt[alleleLeft-1])
 						} else {
-							alleles.Left = tmpVariantRef[0]
+							alleles = append(alleles, tmpVariantRef[0])
 						}
 
 						if ploidy == p.Diploid {
 							if alleleRight > 0 {
-								alleles.Right = tmpVariantAlt[alleleRight-1]
+								alleles = append(alleles, tmpVariantAlt[alleleRight-1])
 							} else {
-								alleles.Right = tmpVariantRef[0]
+								alleles = append(alleles, tmpVariantRef[0])
 							}
 						}