Sentinel Surveillance System Implementation and Evaluation for SARS-CoV-2 Genomic Data, Washington, USA, 2020-2021

Abstract

Genomic data provides useful information for public health practice, particularly when combined with epidemiologic data. However, sampling bias is a concern because inferences from nonrandom data can be misleading. In March 2021, the Washington State Department of Health, USA, partnered with submitting and sequencing laboratories to establish sentinel surveillance for SARS-CoV-2 genomic data. We analyzed available genomic and epidemiologic data during presentinel and sentinel periods to assess representativeness and timeliness of availability. Genomic data during the presentinel period was largely unrepresentative of all COVID-19 cases. Data available during the sentinel period improved representativeness for age, death from COVID-19, outbreak association, long-term care facility-affiliated status, and geographic coverage; timeliness of data availability and captured viral diversity also improved. Hospitalized cases were underrepresented, indicating a need to increase inpatient sampling. Our analysis emphasizes the need to understand and quantify sampling bias in phylogenetic studies and continue evaluation and improvement of public health surveillance systems.

Keywords: COVID-19; SARS; SARS-CoV-2; United States; Washington; coronavirus; coronavirus disease; epidemiology; genomics; respiratory infections; severe acute respiratory syndrome coronavirus 2; surveillance; viruses; zoonoses.

Figure 1

Geographic extent of sequencing data available for COVID-19 cases in study of sentinel surveillance system implementation and evaluation for SARS-CoV-2 genomic data, Washington, USA, 2020–2021. A) Presentinel surveillance (specimens sequenced before March 1, 2021). B) Sentinel surveillance (specimens sequenced on or after March 1, 2021, through the sentinel surveillance program). Standardized ratios (observed/expected counts) of cases with sequenced specimens are indicated by county. No sequence data were available for 3 counties during the presentinel period.

Figure 2

Rarefaction analysis of virus haplotype diversity in Yakima, Clark, and Whatcom Counties in study of sentinel surveillance system implementation and evaluation for SARS-CoV-2 genomic data, Washington, USA, 2020–2021. Presentinel COVID-19 cases (sequenced before March 1, 2021) with sequenced specimens from Yakima County (2 timepoints) were compared with sentinel COVID-19 cases (sequenced on or after March 1, 2021, through the sentinel surveillance program) with sequenced specimens in Clark and Whatcom Counties. Haplotype count indicates virus diversity.

Figure 3

Timeliness of sequence data availability in study of sentinel surveillance system implementation and evaluation for SARS-CoV-2 genomic data, Washington, USA, 2020–2021. Graph shows percentages of COVID-19 cases with sequenced data uploaded to the GISAID database (https://www.gisaid.org) within 0–13, 14–27, and >28 days after specimen collection. A) Presentinel surveillance (specimens sequenced before March 1, 2021). B) Sentinel surveillance (specimens sequenced on or after March 1, 2021, through the sentinel surveillance program).