Table 2.
Coronavirus Disease 2019 Clusters Defined by Epidemiologic and/or a Common Genomic Lineage
| Clustera | Description | Known Cases, No. | Viral Genomes, No.b | Case Abbreviations | Lineage (SNVs) |
|---|---|---|---|---|---|
| A | Solano County clusterc | 4 | 1 | UC195 | Solano County lineage (C9924T) |
| B | Household and HCW-associated cluster of 5 | 5 | 5 | UC101, UC102, UC106, UC120, UC121 | SCC2 lineage (G14718T) |
| C | Household cluster of 9d | 9 | 8 | UC167, UC169, UC170, UC171, UC172, UC173, UC174, UC175 | SCC3 lineage (G26951T and/or C27874T) |
| D | Cluster at local churche | 7 | 3 | UC161, UC197, UC200 | WA1 lineage (C8782T, C18060T, T28144C, C17747T, A17858G) |
| E | Household cluster of 4, including a couple and 2 in-home caregiversf | 4 | 2 | UC149 and UC151 | Wuhan Hu-1 lineage (0 SNVs) |
| F | Parent and child attending a school-hosted gathering (from which there had been other reported cases) | 2 | 2 | UC137 and UC159 | Wuhan Hu-1 lineageg |
| G | SJC airport cluster | 11 | 9 | UC13, UC14, UC15, UC34 and UC143 (workplace); UC16, UC17 (household contacts of UC13); UC117,h UC138 (HCW for UC13 and UC14) | SCC1 lineage (G29711T) |
| H | Grocery store clusteri | 6 | 3 | UC141, UC179, UC196 | SCC1 lineage (G29711T) |
| I | Cluster of 4 includes a parent who traveled to Asia, his child, a tenant, and a friend/coworker of the childj | 4 | 4 | UC135, UC150, UC158, UC166 | SCC1 lineage (G29711T) |
| J | Household cluster of 4, including a couple with history of out-of-state travel and their child | 4 | 3 | UC130, UC139, UC153 | SCC1 lineage (G29711T) |
| K | Two couple-family with history of out-of-state travel | 4 | 2 | UC107 and UC118 | SCC1 lineage (G29711T) |
| L | Household cluster of 3; multigenerational family | 3 | 3 | UC160, UC176, UC178 | SCC1 lineage (G29711T) |
| M | Couple and sibling with history of travel within California | 3 | 3 | UC103, UC110, UC112 | SCC1 lineage (G29711T) |
| N | Couple returning from a trip to the Middle East | 2 | 2 | UC104, UC105 | D614G lineage (A23403G) |
| O | Cruise ship travelers, including a couple and an additional unrelated person [21] | ≥78 | 3 | UC124, UC146, and CZB-1788 | WA1 lineage (C8782T, C18060T, T28144C, C17747T, A17858G) |
Abbreviations: HCW, healthcare worker; SJC airport, San Jose International Airport; SNVs, single-nucleotide variants.
aCluster defined as ≥2 persons with epidemiologic links confirmed by viral whole-genome sequencing (WGS).
bViral genomes from 53 cases, each part of a defined cluster, are shown in this table (the remaining 48 of 101 total cases in this study were not part of a cluster); viral genomes are not available for some cases, as the corresponding clinical specimen was not available for viral WGS.
cThe Solano County cluster (Solano County C9924T lineage) includes Solano County case UC4 from a previous publication [4].
dAnother case (UC155) was assigned to the SCC3 lineage, but there is no known epidemiologic link with the household cluster of 9.
eViral genomic sequencing identified 1 additional case in the cluster, which was missed by contact tracing.
fSamples from the 2 caregivers were not available for sequencing.
gParent and child with 0 SNVs relative to ancestral Wuhan Hu-1 genome.
hReported as UC35 in a previous publication [4].
iGrocery store cluster (SCC1 G29711T lineage) includes Solano County case UC21 from a previous publication [4].
jThe last 3 persons listed are also HCWs.