As one of the current global health conundrums, COVID-19 pandemic caused a dramatic increase of cases exceeding 79 million and 1.7 million deaths worldwide. Severe presentation of COVID-19 is characterized by cytokine storm and chronic inflammation resulting in multi-organ dysfunction. Currently, it is unclear whether extrapulmonary tissues contribute to the cytokine storm mediated-disease exacerbation. In this study, we applied systems immunology analysis to investigate the immunomodulatory effects of SARS-CoV-2 infection in lung, liver, kidney, and heart tissues and the potential contribution of these tissues to cytokines production. Notably, genes associated with neutrophil-mediated immune response (e.g. CXCL1) were particularly upregulated in lung, whereas genes associated with eosinophil-mediated immune response (e.g. CCL11) were particularly upregulated in heart tissue. In contrast, immune responses mediated by monocytes, dendritic cells, T-cells and B-cells were almost similarly dysregulated in all tissue types. Focused analysis of 14 cytokines classically upregulated in COVID-19 patients revealed that only some of these cytokines are dysregulated in lung tissue, whereas the other cytokines are upregulated in extrapulmonary tissues (e.g. IL6 and IL2RA). Investigations of potential mechanisms by which SARS-CoV-2 modulates the immune response and cytokine production revealed a marked dysregulation of NF-κB signaling particularly CBM complex and the NF-κB inhibitor BCL3. Moreover, overexpression of mucin family genes (e.g. MUC3A, MUC4, MUC5B, MUC16, and MUC17) and HSP90AB1 suggest that the exacerbated inflammation activated pulmonary and extrapulmonary tissues remodeling. In addition, we identified multiple sets of immune response associated genes upregulated in a tissue-specific manner (DCLRE1C, CHI3L1, and PARP14 in lung; APOA4, NFASC, WIPF3, and CD34 in liver; LILRA5, ISG20, S100A12, and HLX in kidney; and ASS1 and PTPN1 in heart). Altogether, these findings suggest that the cytokines storm triggered by SARS-CoV-2 infection is potentially the result of dysregulated cytokine production by inflamed pulmonary and extrapulmonary (e.g. liver, kidney, and heart) tissues.

A Gram-stain-positive, aerobic, spore-forming, rod-shaped bacterium, PN2^T, was isolated from a soil sample collected near the Pindari glacier. It contained anteiso-C_15 : 0, iso-C_15 : 0 and C_16 : 1ω7c alcohol as the predominant fatty acids, MK-7 as the major menaquinone and A4α type (l-Lys–d-Glu) peptidoglycan. Based on these characteristics, strain PN2^T was assigned to the genus Paenisporosarcina . Phylogenetic analysis based on 16S rRNA gene sequence placed strain PN2^T within the genus Paenisporosarcina and showed a sequence similarity of 98.5–99.0 % with members of this genus. Paenisporosarcina macmurdoensis CMS 21w^T, Paenisporosarcina quisquiliarum SK 55^T and Sporosarcina antarctica N-05^T were identified as the most closely related species with 16S rRNA gene sequence similarities of 98.6 %, 99.0 % and 98.4 %, respectively. The values for DNA–DNA relatedness between strain PN2^T and P. macmurdoensis , P. quisquiliarum and S. antarctica were below the 70 % threshold value (32.0 %, 42.0 % and 38.0 % respectively). In addition, strain PN2^T exhibited a number of phenotypic differences from P. macmurdoensis , P. quisquiliarum and S. antarctica . Based on the cumulative differences, strain PN2^T was identified as representing a novel species and the name Paenisporosarcina indica sp. nov. was proposed. The type strain of Paenisporosarcina indica sp. nov. is PN2^T (LMG 23933^T = JCM 15114^T). Furthermore, based on the morphological and chemotaxonomic characteristics, the species Sporosarcina antarctica was reclassified as a species of the genus Paenisporosarcina and renamed Paenisporosarcina antarctica comb. nov. In addition, an emended description of the genus Paenisporosarcina is presented.

A novel Gram-negative, rod–coccus shaped, non-motile, strain, RS-3^T, was isolated from a sediment sample collected from the marine transect of Kongsfjorden, Ny-Ålesund, Svalbard, Arctic. Colonies and broth cultures were yellowish in colour due to the presence of carotenoids. Strain RS-3^T was positive for oxidase, aesculinase, caseinase, gelatinase and urease activities and negative for amylase, catalase, lipase, lysine decarboxylase, ornithine decarboxylase, DNase and β-galactosidase activities. The predominant fatty acids were iso-C_15 : 0 (18.0), anteiso-C_15 : 0 (16.8), iso-C_15 : 1 G (14.2), anteiso-C_15 : 1 A (6.0) and iso-C_15 : 0 3-OH (6.8). Strain RS-3^T contained MK-6 (72.42 %) and MK-7 (27.58 %) as the major respiratory quinones and phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids make up the polar lipid composition. The DNA G+C content of strain RS-3^T was 34.7±1.2 mol%. The 16S rRNA gene sequence analysis indicated that Winogradskyella pacifica and Winogradskyella thalassocola are the most closely related species with sequence similarities to the type strains of these species of 98.5 and 97.7 %, respectively. However, DNA–DNA hybridization with Winogradskyella pacifica KCTC 22997^T and Winogradskyella thalassocola DSM 15363^T showed a relatedness of 22 and 42.5 % with respect to strain RS-3^T. Based on the DNA–DNA hybridization values, phenotypic and chemotaxonomic characteristics and phylogenetic inference, strain RS-3^T is proposed as a novel species of the genus Winogradskyella , for which the name Winogradskyella psychrotolerans sp. nov. is proposed. The type strain of Winogradskyella psychrotolerans sp. nov. is RS-3^T ( = CIP 110154^T = NBRC 106169^T). An emended description of the genus Winogradskyella is provided.

A novel Gram-negative, rod-shaped, non-motile, psychrophilic bacterium, designated strain E4-9a^T, was isolated from a marine sediment sample collected at a depth of 276 m from Kongsfjorden, Svalbard, in the Arctic Ocean. The colony colour was golden yellow. Strain E4-9a^T was positive for amylase activity at 5 °C. The predominant fatty acids were iso-C_15 : 1 G (21.8 %), anteiso-C_15 : 0 (19.1 %), anteiso-C_15 : 1 A (18.6 %), iso-C_15 : 0 (13.8 %) and iso-C_16 : 1 H (6.4 %). Strain E4-9a^T contained MK-6 as the major respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids (AL1, AL4 and AL5), an unidentified phospholipid and four unidentified lipids (L1, L4 to L6). Based on 16S rRNA gene sequence similarity, it was ascertained that the closest related species to E4-9a^T were Lacinutrix copepodicola , L. algicola and L. mariniflava , with sequence similarity to the respective type strains of 98.5, 96.5 and 95.8 %. Phylogenetic analysis showed that strain E4-9a^T clustered with the type strain of L. copepodicola and with those of L. algicola and L. mariniflava at distances of 1.5 and 4.8 % (98.5 and 95.2 % similarity), respectively. However, DNA–DNA hybridization with L. copepodicola DJ3^T showed 59 % relatedness with respect to strain E4-9a^T. The DNA G+C content of strain E4-9a^T was 29 mol%. Based on the results of DNA–DNA hybridization and phenotypic data, it appears that strain E4-9a^T represents a novel species of the genus Lacinutrix , for which the name Lacinutrix himadriensis sp. nov. is proposed. The type strain is E4-9a^T ( = CIP 110310^T = KCTC 23612^T).