COVID-19 Variant Update

01 March, 2024

Variants Detected, by Collection Week

As of March 1, 2024, the SARS-CoV-2 Omicron variant JN.1 was continuing to increase in prevalence in the United States, with CDC Nowcast projections estimating further increases in JN.1. At that time, JN.1 was projected to account for more than 95% of COVID-19 infections in the US.

Immunity, Transmissibility and Vaccines: Last Updated March 1, 2024

Evidence from a small serological study has suggested that serological protection against SARS-CoV-2 is reduced against Omicron variants, including XBB.1.5, EG.5.1 and JN.1. However, this study also identified that the JN.1 variant was not associated with further reduced serological protection beyond prior Omicron variants. Another recent study, however, identified the additional capability of JN.1 to evade immune system detection (beyond other Omicron variants).

The JN.1 variant contains several mutations that are associated with escape from vaccine-mediated immune protection. Recent research shows that JN.1 is very efficient at immune evasion, resulting in an increased reproductive number. Vaccination with up-to-date SARS-CoV-2 vaccines does produce antibodies that can recognize JN.1, and vaccination is still effective in preventing severe COVID-19. Research has identified that JN.1 is resistant to monovalent XBB.1.5 vaccine sera, although more recent work has found XBB.1.5 vaccine sera still elicits more neutralizing antibody against JN.1 than non-XBB.1.5-containing vaccine. Preliminary estimates of vaccine effectiveness (VE) against disease likely caused by JN.1 are imprecise due to the recent emergence of JN.1 in the United States. Although those preliminary estimates suggest that there is still substantial VE against JN.1 (VE: 49%; 95% confidence interval: 19 – 68%), the VE estimate is lower than the estimate against non-JN.1 illnesses (VE: 60%; 95% confidence interval: 35 – 75%). These US-based estimates for XBB.1.5 vaccine effectiveness against JN.1 are similar to preliminary estimates from a recent pre-print using data from the Netherlands (41% VE in 18-59-year-olds, and 50% in 60-85 year-olds). JN.1 does appear to be more transmissible but does not appear to cause more severe disease than other SARS-CoV-2 variants.

Due to these combined factors, the Advisory Committee on Immunization Practices recommended in late February 2024 that people 65 years of age and older should get an additional updated COVID-19 vaccine in spring 2024.

Diagnostic Capacity for Variants: Last Updated March 1, 2024

Limited evidence available suggests that COVID-19 antigen and PCR tests are still capable of identifying recently-emerged SARS-CoV-2 variants, such as XBB.1.5, EG.5.1 and JN.1. Reduction or failure of the spike gene amplification in RT-PCR can be used as a (time-dependent) proxy indicator of JN.1 (versus other Omicron lineages) infection.

Therapeutics: Last Updated March 1, 2024

Paxlovid continues to be effective against emerging SARS-CoV-2 variants, including JN.1. 

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