No abstract

Recent studies have highlighted multiple immune perturbations related to severe acute respiratory syndrome coronavirus 2 infection–associated respiratory disease [coronavirus disease 2019 (COVID‐19)]. Some of them were associated with immunopathogenesis of severe COVID‐19. However, reports on immunological indicators of severe COVID‐19 in the early phase of infection in patients with comorbidities such as cancer are scarce. We prospectively studied about 200 immune response parameters, including a comprehensive immune‐cell profile, inflammatory cytokines and other parameters, in 95 patients with COVID‐19 (37 cancer patients without active disease and intensive chemo/immunotherapy, 58 patients without cancer) and 21 healthy donors. Of 95 patients, 41 had severe disease, and the remaining 54 were categorized as having a nonsevere disease. We evaluated the association of immune response parameters with severe COVID‐19. By principal component analysis, three immune signatures defining characteristic immune responses in COVID‐19 patients were found. Immune cell perturbations, in particular, decreased levels of circulating dendritic cells (DCs) along with reduced levels of CD4 T‐cell subsets such as regulatory T cells (T regs ), type 1 T helper (Th1) and Th9; additionally, relative expansion of effector natural killer (NK) cells were significantly associated with severe COVID‐19. Compared with patients without cancer, the levels of terminal effector CD4 T cells, T regs , Th9, effector NK cells, B cells, intermediate‐type monocytes and myeloid DCs were significantly lower in cancer patients with mild and severe COVID‐19. We concluded that severely depleted circulating myeloid DCs and helper T subsets in the initial phase of infection were strongly associated with severe COVID‐19 independent of age, type of comorbidity and other parameters. Thus, our study describes the early immune response associated with severe COVID‐19 in cancer patients without intensive chemo/immunotherapy.

S-gene target failure (SGTF) is neither specific nor accurate for identification of Omicron lineage of SARS-CoV-2. We observed N-gene target failure (NGTF) in 402 out of 412 SARS-CoV2 positive cases from December to mid-January 2022 using a commercially available assay. This phenomenon was not observed with more than 15,000 cases tested previously. We sequenced the genome of five samples with NGTF and compared these results with six cases where NGTF was not seen. We confirm that cases with NGTF were the Omicron lineage while cases with preserved N-gene amplification belonged to Delta lineage. We discovered that the ERS31-33 deletion (nucleotide 28362-28370del) overlaps with N gene probe used, explaining NGTF. As the 'stealth' Omicron variant also harbors ERS31-33 deletion, this approach will work for the detection of 'stealth' Omicron variant as well. We suggest that NGTF can be used as a low cost, rapid screening strategy for detection of Omicron.