A viral metagenomic analysis of five surface and two bottom water (878 meters below surface, mbs, and 3,357 mbs) samples from Prydz Bay, was conducted during February–March 2015. The results demonstrated that most of the DNA viruses were dsDNA viruses (79.73–94.06%, except at PBI1, 37.51%). Of these, Caudovirales (Siphoviridae, Myoviridae, and Podoviridae) phages were most abundant in surface seawater (67.67–71.99%), while nucleocytoplasmic large DNA viruses (NCLDVs) (Phycodnaviridae, Mimiviridae, and Pandoraviridae accounted for >30% of dsDNA viruses) were most abundant in the bottom water (3,357 mbs). Of the ssDNA viruses, Microviridae was the dominant family in PBI2, PBI3, PBOs, and PBI4b (57.09–87.55%), while Inoviridae (58.16%) was the dominant family in PBI1. Cellulophaga phages (phi38:1 and phi10:1) and Flavobacterium phage 11b, infecting the possible host strains affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, were abundant in surface water dsDNA viromes. The long contig (PBI2_1_C) from the viral metagenomes were most similar to the genome architectures of Cellulophaga phage phi10:1 and Flavobacterium phage 11b from the Arctic Ocean. Comparative analysis showed that the surface viral community of Prydz Bay could be clearly separated from other marine and freshwater environments. The deep sea viral community was similar to the deep sea viral metagenome at A Long-term Oligotrophic Habitat Assessment Station (ALOHA, at 22°45′N, 158°00′W). The multivariable analysis indicated that nutrients probably played an important role in shaping the local viral community structure. This study revealed the preliminary characteristics of the viral community in Prydz Bay, from both the surface and the deep sea. It provided evidence of the relationships between the virome and the environment in Prydz Bay and provided the first data from the deep sea viral community of the Southern Ocean.
Viruses are the most abundant biological entities in aquatic ecosystems and harbor an enormous amount of genetic diversity. Whereas their influence on marine ecosystems is widely acknowledged, current information about their diversity remains limited. We conducted a viral metagenomic analysis of water samples collected during the austral summer of 2016 from the South Scotia Ridge (SSR), near the Antarctic Peninsula. The taxonomic composition and diversity of the viral communities were investigated, and a functional assessment of the sequences was performed. Phylotypic analysis showed that most viruses belonged to the order Caudovirales, especially the family Podoviridae (41.92–48.7%), which is similar to the situation in the Pacific Ocean. Functional analysis revealed a relatively high frequency of phage-associated and metabolism genes. Phylogenetic analyses of phage TerL and Capsid_NCLDV (nucleocytoplasmic large DNA viruses) marker genes indicated that many sequences associated with Caudovirales and NCLDV were novel and distinct from known phage genomes. High Phaeocystis globosa virus virophage (Pgvv) signatures were found and complete and partial Pgvv-like were obtained, which influence host–virus interactions. Our study expands existing knowledge of viral communities and their diversities from the Antarctic region and provides basic data for further exploring polar microbiomes.
HighlightsOf all, 4,560 viral populations were identified Many virus-encoded auxiliary metabolic genes were predicted Qinghai-Tibet plateau and bathypelagic ocean might represent a viral habitat
Background: The liver-specific microRNA-122 (miR-122) has been demonstrated as a powerful and promising biomarker of hepatic diseases. However, the researches on the accuracy of miR122 detection in chronic viral hepatitis have been inconsistent, leading us to conduct this meta-analysis to systematically summarize the diagnostic value of circulating miR-122 in patients with hepatitis B virus (HBV) and/or hepatitis C virus (HCV)-associated chronic viral hepatitis. Methods: A comprehensive literature search (updated to January 30, 2019) in PubMed, Cochrane library, EMBASE, CNKI, Wanfang, and CQVIP databases was performed to identify eligible studies. The sensitivity (SEN), specificity (SPE), positive and negative likelihood ratios (PLR and NLR), diagnostic odds ratio (DOR), and area under the curve (AUC) were pooled to explore the diagnostic performance of circulating miR-122. Subgroup and threshold effect analysis were further carried out to explore the heterogeneity. Results: Overall, 15 studies were finally included in this meta-analysis according to the exclusion and inclusion criteria. The pooled estimates indicated a moderately high diagnostic accuracy for circulating miR-122, with a sensitivity of 0.92 [95% confidence interval (CI), 0.86–0.95], a specificity of 0.84 (95% CI, 0.78–0.89), a PLR of 5.7 (95% CI, 4.7–8.1), a NLR of 0.1 (95% CI, 0.06–0.18), a DOR of 57 (95% CI 25-129), and an AUC of 0.93 (95% CI, 0.91–0.95). The subgroup analysis demonstrated that diagnostic accuracy was better for HCV-associated chronic viral hepatitis patients and non-Chinese compared with other subgroups. In addition, we found that serum might be a more promising matrix for detecting the expression of miR-122 than plasma. Conclusions: Our results demonstrated that circulating miR-122 have a relatively high diagnostic value for chronic viral hepatitis detection, especially in the patients with HCV-associated chronic viral hepatitis. However, further large cohort studies are still required to confirm our findings.
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