No abstract

Vaccines against SARS-CoV-2 have shown high efficacy in clinical trials, yet a full immunologic characterization of these vaccines, particularly within the upper respiratory tract, remains lacking. We enumerated and phenotyped T cells in nasal mucosa and blood before and after vaccination with the Pfizer-BioNTech COVID-19 vaccine (n =21). Tissue-resident memory (Trm) CD8+ T cells expressing CD69+CD103+ expanded ~12 days following the first and second doses, by 0.31 and 0.43 log10 cells per swab respectively (p=0.058 and p=0.009 in adjusted linear mixed models). CD69+CD103+CD8+ T cells in the blood decreased post-vaccination. Similar increases in nasal CD8+CD69+CD103- T cells were observed, particularly following the second dose. CD4+ Th17 cells were also increased in abundance following both doses. Following stimulation with SARS-CoV-2 spike peptides, CD8+ T cells increased expression of CD107a and CD154. These data suggest that nasal T cells may be induced and contribute to the protective immunity afforded by this vaccine.

61. CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/278374 doi: bioRxiv preprint first posted online Mar. 8, 2018; and directly test the two competing hypotheses. We find that early genomes from Asian phenotypic affinity, suggesting that human diversity in SEA was strongly influenced by 82 population expansions from the north (4). Yet, the extent to which the movements from East 83 Asia (EA) impacted on the genetic and cultural makeup of the people of SEA remains 84 controversial. 85Two distinct population models have been proposed to account for the biological and was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. hybridisation to baits that cover the entire mappable human genome (15). 119We performed comparative testing of three different capture approaches for human was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/278374 doi: bioRxiv preprint first posted online Mar. 8, 2018; Biosciences) -with the aim of applying the most effective method to ancient human remains 124 from tropical SEA (SOM1). We found a modified version of MYbaits Whole Genome 125Enrichment to be the best-performing method. We applied this method, in combination with 126 shotgun sequencing approaches where sufficient endogenous DNA allowed it, to samples from 127 Malaysia, Thailand, Philippines, Vietnam, Indonesia and Laos, dating between 0.2 and 8 kya 128 (SOM2). We obtained 25 low-coverage ancient genomes (Table 1), along with mtDNA and 129 nuclear DNA from an additional set of 16 individuals (Table S3), belonging to hunter-gatherers 130 from the Hoabinhian culture, as well as Neolithic, Bronze Age and Iron Age farmers (SOM3). 131All samples showed damage patterns typical of ancient DNA (38) ( Table S3). 132To address the genetic relationships among the ancient individuals, we performed a constructed solely with present-day samples (40) (SOM4). We then used ADMIXTURE (41) 136 to find reference latent ancestry components that could best fit our present-day data, and then Vietnam, Laos and Thailand) populations, along with a broad East Asian component. 152We used outgroup f3 statistics (f3(Mbuti;X,Ancient samples)) to determine which 153 populations have the highest levels of shared drift with each of the ancient individuals (SOM6). 154. CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/278374 doi: bioRxiv preprint first posted online Mar. 8, 2018; Group 1 shares the most drift with certain ancient mainland samples ( ...