Evolutionary Perspective and Theories on the Possible Origin of SARS-CoV-2.

OBJECTIVE: From the currently available next-generation sequencing data, we have tried to analyze different theories on the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and thereby to identify the origin of its intermediate host. Genome sequence-based phylogenetic analysis and multiple sequence alignment were performed. METHODS: We used the Virus Pathogen Resource (ViPR) platform for phylogenetic analysis and the MUltiple Sequence Comparison by Log- Expectation (MUSCLE) algorithm for whole genome sequence alignment of SARS-CoV-2, severe acute respiratory syndrome coronavirus (SARS-CoV), BJ01, Middle East respiratory syndrome coronavirus (MERS-CoV), bat coronavirus RaTG13, and pangolin coronavirus. RESULTS: From these two analyses, we have found that RaTG13 is the closest relative to SARS-CoV-2 and not the pangolin coronavirus in spite of having sequence homology-based similarity in the genes. Comparing the RNA-dependent RNA polymerase (RdRp) and interacting spike (S) protein that interacts directly with the host human angiotensin-converting enzyme 2 (hACE2), the bat coronavirus RaTG13 was found to be the closest relative to SARS-CoV-2. Through multiple sequence alignment of the amino acid sequences, we found the furin-like cleavage site RRARS only in SARS-CoV-2 at the junction of the two subunits S1/S2 of the spike protein. CONCLUSIONS: The possible zoonotic transfer that has happened in SARS-CoV-2 seems to not be from the pangolin, but RaTG13 remains closest relative to SARS-CoV-2. Further studies, such as systematic reviews of the literature and meta-analyses, are needed to reach a conclusion regarding the evolutionary trajectory of the SARS-CoV-2 outbreak.

Elevated serum activity of MBL and ficolin-2 as biomarkers for progression to hepatocellular carcinoma in chronic HCV infection.

Hepatocellular carcinoma (HCC) is an uncommon but significant outcome of chronic hepatitis C virus (HCV) infection. A serum biomarker for predicting progression to HCC would have a major impact on patient monitoring and clinical management. We explored circulating liver-expressed lectins, ficolin-2, ficolin-3 and mannose binding lectin (MBL), as potential biomarkers for the development of HCC. The activity of these three lectins were analysed in HCV positive patients who developed HCC (n = 31) with comparable HCV-positive HCC-negative patients (n = 106) and healthy controls (n = 79). Serum binding activity of ficolin-2 and MBL were elevated compared to controls. Analysis of pre-HCC onset samples revealed that MBL levels were significantly elevated up to 3 years, and ficolin-2 was elevated up to 1 year, prior to diagnosis of HCC over controls. This preliminary study identifies MBL and ficolin-2 as potential biomarkers for the development of HCC in chronic HCV infection.

Expression of human ficolin-2 in hepatocytes confers resistance to infection by diverse hepatotropic viruses.

The liver-expressed pattern recognition receptors mannose-binding lectin (MBL), ficolin-2 and ficolin-3 contribute to the innate immune response by activating complement. Binding of soluble ficolin-2 to viral pathogens can directly neutralize virus entry. We observed that the human hepatoma cell line HuH7.5, which is routinely used for the study of hepatotropic viruses, is deficient in expression of MBL, ficolin-2 and ficolin-3. We generated a cell line that expressed and secreted ficolin-2. This cell line (HuH7.5 [FCN2]) was more resistant to infection with hepatitis C virus (HCV), ebolavirus and vesicular stomatitis virus, but surprisingly was more susceptible to infection with rabies virus. Cell-to-cell spread of HCV was also inhibited in ficolin-2 expressing cells. This illustrates that ficolin-2 expression in hepatocytes contributes to innate resistance to virus infection, but some viruses might utilize ficolin-2 to facilitate entry.