SARS-CoV-2 Sequencing and Variants in Washington State Washington State Department of Health April 13, 2022 Next generation sequencing is a set of laboratory methods that scientists use to scan a viral genome to determine the genome sequence of a virus. A genome sequence of a virus is referred to as its “genomic fingerprint,” and can reveal mutations in a virus that make it unique. Mutations are changes in a genome sequence and occur naturally over time. Scientists compare viral genomes to better understand how viruses can spread from person to person. Sequencing allows public health officials to detect clusters of cases, and monitor new lineages. Groups of same-species viruses that share a set of genome mutations are referred to as a lineage. Some lineages may have characteristics such as the ability to spread more quickly, or cause more severe disease. These lineages are classified as variants of interest, variants being monitored, or variants of high concern. Throughout this report, we refer to the scientific name of the virus SARS-CoV-2 that causes COVID-19. Sequencing can only be performed on samples that are processed in laboratories and where swabs are stored in liquid that is compatible with sequencing, which means only samples used for molecular tests (such as PCR) can be included. For this reason, this report is limited to confirmed cases only. The genomes that are sequenced and compared are those of the virus, not humans. At a glance (data through April 12, 2022) • During the month of March 2022, 15.1% 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. • 82,911 (8.3%) COVID-19 cases in Washington state have sequencing information available since January 2021. 4 Page break CDC currently categorizes variants as Variants of High Consequence (VOHC), Variants of Concern (VOC), Variants of Interest (VOI) and Variants Being Monitored (VBM). There are currently no VOHC and VOI so only VOC and VBM are detailed in this report. Variants of Concern Variant Area first detected Background Cumulative Washington cases detected First detection in Washington* Most recent detection in Washington* Delta (B.1.617.2 and AY lineages) India Delta has been found to be more transmissible than other variants such as Alpha, and some research indicates greater risk of hospitalization. Approved vaccines are effective at preventing severe disease and death, including against the Delta variant. 38,107 Apr 03, 21 Feb 28, 22 Omicron (B.1.1.529 and BA lineages) South Africa Early research indicates evidence for increased transmissibility, immune evasion, and lower risk of hospitalization and death, relative to Delta. Approved vaccines are effective at preventing severe disease and death, including against the Omicron variant. 21,093 Nov 29, 21 Mar 29, 22 *Detection dates are based on the date a sample is collected, it can take several weeks before a variant result is completed and added to the report Variants being monitored Variant ction dates are based on the date a sample is collected, it can take several weeks before a variant result is completed and added to the report 5 Page break Epidemiologic curve of variants being monitored and variants of concern by week of specimen collection date from January 01, 2021 to April 02, 2022 • The above graph shows the total number of variants detected by the week the specimen was collected from a patient. • Sequencing can be performed on stored patient specimens at any time, so these numbers may change as additional specimens are sequenced. • This graph shows all specimens sequenced, including specimens sequenced during outbreaks and other targeted sequencing efforts. 6 Page break Number of specimens sequenced, and percent of Washington State confirmed COVID-19 cases that have been sequenced by specimen collection date from January 2021 through March 2022. • Samples are not sequenced for every confirmed COVID-19 case. The above graph shows the total number of specimens sequenced (gray bars) and the percent of all confirmed cases (blue line) that have had sequencing performed each month. Data from the previous month may still be incomplete. • Sequencing can be performed on stored specimens at any time, so numbers from past months may change if stored specimens are sequenced. 7 Page break SARS-CoV-2 Lineages Circulating in Washington State The graph below shows the change in proportion of select SARS-CoV-2 lineages by time period. A viral lineage is a group of viruses that descend from a common ancestor with shared genetic characteristics, allowing them to be grouped together. There are many different virus lineages that are not variants of concern or variants being monitored. These are grouped together as ‘Other’ on this chart. As the proportions of variants increase, the proportion of other lineages will decrease. NOTE: The data on this graph come from cases that are randomly selected for sequencing statewide; cases sequenced