C Proteins: Controllers of Orderly Paramyxovirus Replication and of the Innate Immune Response

Particles of many paramyxoviruses include small amounts of proteins with a molecular weight of about 20 kDa. These proteins, termed “C”, are basic, have low amino acid homology and some secondary structure conservation. C proteins are encoded in alternative reading frames of the phosphoprotein gene. Some viruses express nested sets of C proteins that exert their functions in different locations: In the nucleus, they interfere with cellular transcription factors that elicit innate immune responses; in the cytoplasm, they associate with viral ribonucleocapsids and control polymerase processivity and orderly replication, thereby minimizing the activation of innate immunity. In addition, certain C proteins can directly bind to, and interfere with the function of, several cytoplasmic proteins required for interferon induction, interferon signaling and inflammation. Some C proteins are also required for efficient virus particle assembly and budding. C-deficient viruses can be grown in certain transformed cell lines but are not pathogenic in natural hosts. C proteins affect the same host functions as other phosphoprotein gene-encoded proteins named V but use different strategies for this purpose. Multiple independent systems to counteract host defenses may ensure efficient immune evasion and facilitate virus adaptation to new hosts and tissue environments.

Identifying Inconclusive Data in the SARS-CoV-2 Molecular Diagnostic Using Nucleocapsid Phosphoprotein Gene as Target

ABSTRACT Context: The gold standard test to identify the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in coronavirus disease 2019 (COVID-19) patients is the real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR), but the inconclusive data and presence of false positive diagnosis remain the major problem of this approach. Objective: To compare the fitness of two primers sets to the SARS-CoV-2 nucleocapsid phosphoprotein (NP) gene in the molecular diagnosis of COVID-19, we verify the inconclusive data and confidence of high cycle threshold (Ct) values in the SARS-CoV-2 detection. Design: The 970 patient samples were tested using United States Centers for Disease Control and Prevention protocol. We compared the fitness of two primers sets to two different regions of NP gene. In addition, we check the consistency of positive samples with high Ct values by retesting extracted SARS-CoV-2 RNA or by second testing of patients. Results: The N1 and N2 displayed similar fitness during testing with no differences between Ct values. Then, we verified security range Cts related to positive diagnostic with Ct above 34 failing in 21/32 (65.6%) after retesting of samples. The samples patients with Ct above 34.89 that were doubly positive revealed a low sensitivity (52.4%) and specificity (63.6%) of the test in samples with Ct above 34. Conclusions: It is secure to use one primer set to the NP gene to identify SARS-CoV-2 in samples. However, samples with high Ct values may be considered inconclusive and retested to avoid false positive diagnosis.

Evolutionary History of Cotranscriptional Editing in the Paramyxoviral Phosphoprotein Gene

The phosphoprotein gene of the paramyxoviruses encodes multiple protein products. The P, V, and W proteins are generated by transcriptional slippage. This process results in the insertion of non-templated guanosine nucleosides into the mRNA at a conserved edit site. The P protein is an essential component of the viral RNA polymerase, and is encoded by a faithful copy of the gene in the majority of paramyxoviruses. However, in some cases the non essential V protein is encoded by default and guanosines must be inserted into the mRNA in order to encode P. The number of guanosines inserted into the P gene can be described by a probability distribution which varies between viruses. In this article we review the nature of these distributions, which can be inferred from mRNA sequencing data, and reconstruct the evolutionary history of cotranscriptional editing in the paramyxovirus family. Our model suggests that, throughout known history of the family, the system has switched from a P default to a V default mode four times; complete loss of the editing system has occurred twice, the canonical zinc finger domain of the V protein has been deleted or heavily mutated a further two times, and the W protein has independently evolved a novel function three times. Finally, we review the physical mechanisms of cotranscriptional editing via slippage of the viral RNA polymerase.

Correction to: Determining the effects of trastuzumab, cetuximab and afatinib by phosphoprotein, gene expression and phenotypic analysis in gastric cancer cell lines

An amendment to this paper has been published and can be accessed via the original article.

Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene

The phosphoprotein gene of the paramyxoviruses encodes multiple protein products. The P, V, and W proteins are generated by transcriptional slippage. This process results in the insertion of non-templated guanosine nucleosides into the mRNA at a conserved edit site. The P protein is an essential component of the viral RNA polymerase, and is encoded by a direct copy of the gene in the majority of paramyxoviruses. However, in some cases the non-essential V protein is encoded by default and guanosines must be inserted into the mRNA in order to encode P. The number of guanosines inserted can be described by a probability distribution which varies between viruses. In this article we review the nature of these distributions, which can be inferred from mRNA sequencing data, and reconstruct the evolutionary history of cotranscriptional editing in the paramyxovirus family. Our model suggests that, throughout known history of the family, the system has switched from a P default to a V default mode four times; complete loss of the editing system has occurred twice, the canonical zinc finger domain of the V protein has been deleted or heavily mutated a further two times, and the W protein has independently evolved a novel function three times. Finally, we review the physical mechanisms of cotranscriptional editing via slippage of the viral RNA polymerase.

Phosphoprotein gene of peste des petits ruminants virus: unsuitable for lineage determination

The aim of this study was to investigate the effect of isoflurane (ISO) and sevoflurane (SEVO) anesthesia on coagulation parameters in dogs. A total of 12 dogs were used in the study in two groups as ISO(n = 6) and SEVO(n = 6), which were brought to the clinic for ovariohysterectomy. Premedication was performed by the intravenous administration of 0.3 mg/kg midazolam, followed by 5 mg/kg intravenous bolus propofol infusion. This was followed by 1.5% ISO administration in the ISO group and 2% sevoflurane administration in the SEVO group for anesthesia maintenance. Before anesthesia, prothrombin time (PT), active partial thromboplastin time (APTT), thrombin time (TT), and fibrinogen (FIB) level were measured at the 0th minute before anesthesia, at the 15th and 30th minutes during anesthesia, and at the 0th minute and the 1st hour after anesthesia. It was observed that the changes in TT, PT, APTT, and FIB level with time were not significant in the ISO and SEVO groups. It was determined that the changes in TT between the measurements in groups at the 30th minute during anesthesia and 0th minute after anesthesia were statistically significant (P less than 0.05)

Morbillivirus-associated lipid pneumonia in Arctic foxes

We describe lipid pneumonia in 5 of 24 Arctic foxes ( Vulpes lagopus) in association with morbillivirus infection, and lymphoid depletion in 3 of these 5 foxes. Canine distemper virus (CDV) immunohistochemistry yielded positive staining in lung, lymph nodes, spleen, adipose tissue, and renal pelvic urothelial cells in 5 cases. Liver and bone marrow samples collected from these cases tested positive for morbillivirus by reverse-transcription PCR assay. Strains belonged to the CDV Arctic lineage based on sequencing of the hemagglutinin gene followed by phylogenetic analysis. Phylogenetic analysis of the phosphoprotein gene showed that the identified CDV strains were not closely related to any previously documented strains responsible for outbreaks in different animals in other parts of the world.