Skip to main content
. 2021 Aug 27;70(34):1170–1176. doi: 10.15585/mmwr.mm7034e5

FIGURE 2.

This figure includes one bar chart showing SARS-CoV-2 whole genome sequencing lineage results for five variants, by vaccination status, and three box and whisker plots showing reverse transcription–polymerase chain reaction cycle threshold values for three gene targets, by vaccination status, for specimens from Los Angeles County, California, during May 1–July 25, 2021.

SARS-CoV-2 whole genome sequencing lineage results* and reverse transcription–polymerase chain reaction cycle threshold values† for two gene targets,§ by vaccination status and month — Los Angeles County, California, May 1–July 25, 2021

Abbreviations: Ct = cycle threshold; N = nucleocapsid; ORF1ab = open reading frame 1 ab; RT-PCR = reverse transcription–polymerase chain reaction; SC2N = SARS-CoV-2 nucleocapsid.

* SARS-CoV-2 infections among Los Angeles County residents aged ≥16 years with whole genome sequencing lineage results (n = 6,752) for fully vaccinated (n = 1,667), partially vaccinated (n = 198), and unvaccinated (n = 4,887) persons.

† Whiskers represent minimum and maximum observations; top of box represents the third quartile, bottom represents the first quartile, and box height represents the interquartile range. The midline is the median.

§ Ct values are correlated with the amount of viral nucleic acid present. Gene targets for RT-PCR testing included the N protein gene region and the ORF1ab polyprotein gene region. The N gene targets were analyzed separately for two laboratories because Ct values are not directly comparable across different testing laboratories; these N gene targets were designated SC2N and N to differentiate between the two participating laboratory partners. Gene targets were selected based on testing platforms used by Los Angeles County Department of Public Health laboratory partners. Analysis of SC2N Ct values is restricted to a Fulgent test result with a Ct value on the same day as person’s first positive RT-PCR test result; SC2N gene target values (n = 5,179) are stratified for fully vaccinated (n = 1,248), partially vaccinated (n = 151), and unvaccinated (n = 3,780) persons. Analysis of ORF1ab and N Ct values is restricted to a Valencia Branch Laboratory test result with a Ct value on the same day as person’s first positive RT-PCR test result. ORF1ab (n = 1,041) and N (n = 1,062) gene target values are stratified for fully vaccinated (n = 289 and n = 297, respectively), partially vaccinated (n = 36 and n = 41, respectively), and unvaccinated (n = 716 and n = 724, respectively) persons.

Persons were considered fully vaccinated ≥14 days after receipt of the second dose in a 2-dose series (Pfizer-BioNTech or Moderna COVID-19 vaccines) or after 1 dose of the single-dose Janssen (Johnson & Johnson) COVID-19 vaccine; partially vaccinated ≥14 days after receipt of the first dose and <14 days after the second dose in a 2-dose series; and unvaccinated <14 days receipt of the first dose of a 2-dose series or 1 dose of the single-dose vaccine or if no vaccination registry data were available.