Early Mucosal Type II Interferon Limits SARS-CoV-2 Replication in Humans

COVID-19 vaccines markedly reduce disease severity, but their ability to block infection and transmission remains limited and variable. ¹ A better understanding of early mucosal immune programs that constrain viral replication at susceptible upper respiratory sites is needed to develop more effective antiviral strategies. However, temporal and anatomical antiviral dynamics are difficult to resolve without longitudinal, paired-site sampling beginning before infection onset. We quantified longitudinal viral load by RT-qPCR and human gene expression by mRNA sequencing in 1,237 samples prospectively collected daily from the nasal cavity, oral cavity, and oropharynx of 16 individuals starting from the onset of naturally acquired SARS-CoV-2 infection, and 16 age-, sex-, and vaccination-matched uninfected individuals. Here we show that Type I interferon (IFN) responses are initiated concurrently across these upper respiratory sites, even before local viral detection. In contrast, Type II IFN initiation is more spatially variable, and earlier nasal Type II IFN initiation is associated with reduced viral replication, prior COVID-19 vaccination, and higher tissue-resident memory T cell (T _RM ) signature expression. These findings demonstrate that in addition to humoral immunity, prior vaccination primes rapid, inducible mucosal Type II IFN responses, likely mediated by rare T _RM upon viral encounter, to limit viral replication and spread.

Using a unique study design with temporally-dense, paired sampling of the oral cavity, nasal cavity and oropharynx from the onset of naturally acquired human SARS-CoV-2 infection, we demonstrate that Type I IFN responses are initiated synchronously in the upper respiratory mucosa during early infection, whereas the timing of Type II IFN response initiation is asynchronous but earlier initiation is associated with prior COVID-19 vaccination, enhanced tissue-resident memory T cells signatures, and reduced local viral replication.

Among participants who prospectively collected daily, paired specimens from multiple upper respiratory anatomical sites while enrolled in a case-ascertained COVID-19 household transmission study conducted in Los Angeles, California between September 2020 and April 2022, a subset of participants were found to initially be negative upon enrollment but later became positive for SARS-CoV-2. These were defined as Cases of naturally acquired, incident SARS-CoV-2 infection, and for whom age, sex, and prior COVID-19 vaccination status matched Control participants without SARS-CoV-2 infection were identified, and demographic data is shown. Samples underwent viral load quantification by RT-qPCR, validated by RT-ddPCR, and human transcriptome sequencing to calculate immune pathway activation and determine the timing of Type I and II IFN response initiation, and expression of a tissue resident memory T cell (T _RM ) signature. Differences in the magnitude and timing of these pathways were compared by vaccination status, and by subsequent viral RNA shedding to identify mucosal immune correlates of reduced viral replication. Created in https://BioRender.com .