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

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.

Changing genomic epidemiology of COVID-19 in long-term care facilities during the 2020–2022 pandemic, Washington State

Background

Long-term care facilities (LTCFs) are vulnerable to disease outbreaks. Here, we jointly analyze SARS-CoV-2 genomic and paired epidemiologic data from LTCFs and surrounding communities in Washington state (WA) to assess transmission patterns during 2020–2022, in a setting of changing policy. We describe sequencing efforts and genomic epidemiologic findings across LTCFs and perform in-depth analysis in a single county.

SARS-CoV-2 Sequencing and Variants in Washington State - November 2023

At a glance (data through November 28, 2023)

  • During the month of October 2023, 2.3% of all confirmed molecular COVID-19 cases were sequenced. This number is preliminary and will change over time as additional specimens are received from the previous month.
  • 143,210 (9.7%) COVID-19 cases in Washington state have sequencing information available since January 2021.

April 2023 SARS-CoV-2 Sequencing and Variants Report

SARS-CoV-2 Sequencing and Variants Report for March, 2023

 

At a glance (data through March 28, 2023)

  • During the month of February 2023, 12.8% of all confirmed molecular COVID-19 cases were sequenced. This number is preliminary and will change over time as additional specimens are received from the previous month.
  • 139,195 (9.9%) COVID-19 cases in Washington state have sequencing information available since January 2021.

May 2023 SARS-CoV-2 Sequencing and Variants Report

Quantifying transmission intensity and heterogeneity is crucial to ascertain the threat posed by infectious diseases and inform the design of interventions. Methods that jointly estimate the reproduction number R and the dispersion parameter k have however mainly remained limited to the analysis of epidemiological clusters or contact tracing data, whose collection often proves difficult. Here, we show that clusters of identical sequences are imprinted by the pathogen offspring distribution, and we derive an analytical formula for the distribution of the size of these clusters.

Associations Between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants and Risk of Coronavirus Disease 2019 (COVID-19) Hospitalization Among Confirmed Cases in Washington State: A Retrospective Cohort Study

Using a retrospective cohort study, we assessed the hospitalization risk following infection with 7 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants.
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