Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus).

White-tailed deer (WTD) are susceptible to SARS-CoV-2 and represent an important species for surveillance. Samples from WTD (n = 258) collected in November 2021 from Québec, Canada were analyzed for SARS-CoV-2 RNA. We employed viral genomics and host transcriptomics to further characterize infection and investigate host response. We detected Delta SARS-CoV-2 (B.1.617.2) in WTD from the Estrie region; sequences clustered with human sequences from October 2021 from Vermont, USA, which borders this region. Mutations in the S-gene and a deletion in ORF8 were detected. Host expression patterns in SARS-CoV-2 infected WTD were associated with the innate immune response, including signaling pathways related to anti-viral, pro- and anti-inflammatory signaling, and host damage. We found limited correlation between genes associated with innate immune response from human and WTD nasal samples, suggesting differences in responses to SARS-CoV-2 infection. Our findings provide preliminary insights into host response to SARS-CoV-2 infection in naturally infected WTD.

Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission.

Wildlife reservoirs of broad-host-range viruses have the potential to enable evolution of viral variants that can emerge to infect humans. In North America, there is phylogenomic evidence of continual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-tailed deer (Odocoileus virginianus) through unknown means, but no evidence of transmission from deer to humans. We carried out an observational surveillance study in Ontario, Canada during November and December 2021 (n = 300 deer) and identified a highly divergent lineage of SARS-CoV-2 in white-tailed deer (B.1.641). This lineage is one of the most divergent SARS-CoV-2 lineages identified so far, with 76 mutations (including 37 previously associated with non-human mammalian hosts). From a set of five complete and two partial deer-derived viral genomes we applied phylogenomic, recombination, selection and mutation spectrum analyses, which provided evidence for evolution and transmission in deer and a shared ancestry with mink-derived virus. Our analysis also revealed an epidemiologically linked human infection. Taken together, our findings provide evidence for sustained evolution of SARS-CoV-2 in white-tailed deer and of deer-to-human transmission.

COVID-19 Vaccines: How Efficient and Equitable Was the Initial Vaccination Process?

With nearly 11 billion doses of the COVID-19 vaccine being administered, stark differences in the vaccination rates persist. Vaccine distribution initiatives such as COVAX and African Vaccine Acquisition Trust (AVAT) were formed to ensure equitable vaccine delivery. This review evaluates the initial COVID-19 vaccination efforts and the impact of different vaccine distribution initiatives on equitable vaccination coverage in the early phase. We conducted a descriptive and trend analysis with sub-groups by various context parameters of data on COVID-19 vaccination from December 2020 till February 2022, from four public databases including UNICEF, WHO, COVID-19 Task Force and Our World in Data to examine COVID-19 vaccine distribution progress and the contributions of vaccine procurement initiatives. We found that High Income Countries (HICs) had much higher vaccination rate (78.4%) than Lower-Middle-Income Countries (LMICs) (55.5%) and Low-Income Countries (LICs) (10.9%). Large differentials (>80% to <10%) in the vaccination rates of eligible population of adults in LMICs and LICs existed. Differentials in the total vaccine doses delivered to each country ranged from 355.6% to 4.8% of the total population. In LICs, 53.3% of the total doses were obtained via COVAX, 30.9% by bilateral/multilateral agreements, 6.5% by donations and 3.8% by AVAT. In LMICs, 56.4% of total vaccines procured were via bilateral/multilateral agreements, 21.4% by COVAX, 4.2% by donations and 0.5% by AVAT. COVAX delivered 1 billion doses by January 2022 which constituted 53.2% and 21.4% of procured doses in LICs and LMICs. In LICs and LMICs, 6.5% and 4.2% of total doses were acquired through donations while 30.9% and 56.4% of doses were purchased. Despite global efforts, significant disparities were present in COVID-19 vaccination efforts amongst countries of different income groups. Future efforts should focus on addressing vaccine inequities explicitly and in improving global vaccine distribution.