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.

Design, Synthesis, and Evaluation of Functionalized 5-(4-arylpiperazin-1-yl)-N-Quinolinyl-pentanamides as Selective Dopamine D3 Receptor Ligands

Dopamine (1) plays a key role in normal physiological pathways in both the central nervous system and the periphery. The physiological impact of this neurotransmitter is mediated through its interaction with family of G-protein-coupled receptors (GPCRs). These receptors are designated as D1, D2, D3, D4, and D5 and divided into two sub-families, the D1-like sub-family (D1 and D5) and D2-like sub-family (D2, D3 and D4) based on pharmacological properties, amino acid homology, and genetic organization. Aberrant D3 activity has been linked to multiple diseases and conditions such as depression, schizophrenia, substance use disorder, inflammatory diseases, and Parkinson’s disease (PD). As part of our on-going program focused on the identification of novel D3 ligands, we have identified a novel series of 5-(4-arylpiperazin-1-yl)-N-quinolinyl-pentanamides that are high affinity ligands for this receptor.

Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe

The source of the COVID-19 pandemic is unknown, but the natural host of the progenitor sarbecovirus is thought to be Asian horseshoe (rhinolophid) bats. We identified and sequenced a novel sarbecovirus (RhGB01) from a British horseshoe bat, at the western extreme of the rhinolophid range. Our results extend both the geographic and species ranges of sarbecoviruses and suggest their presence throughout the horseshoe bat distribution. Within the spike protein receptor binding domain, but excluding the receptor binding motif, RhGB01 has a 77% (SARS-CoV-2) and 81% (SARS-CoV) amino acid homology. While apparently lacking hACE2 binding ability, and hence unlikely to be zoonotic without mutation, RhGB01 presents opportunity for SARS-CoV-2 and other sarbecovirus homologous recombination. Our findings highlight that the natural distribution of sarbecoviruses and opportunities for recombination through intermediate host co-infection are underestimated. Preventing transmission of SARS-CoV-2 to bats is critical with the current global mass vaccination campaign against this virus.

Molecular Identification of Sweet potato virus C on Sweetpotato in Bali, Indonesia

A survey was conducted in several sweet potato cultivations in Bali Province. Survey found that many plants exhibited potyvirus symptom, such as chlorosis blotches. This study was to determine disease incidence, detection and identification of the virus causing these symptoms on sweet potato plants in Bali. Samples were collected by purposive sampling of 10 plants from each location in Bali (Denpasar, Gianyar, Badung, Buleleng, Tabanan, Klungkung, Karangasem, Jembrana, Bangli). Disease insidence was observed based on viral symptoms in the field. Identification of nucleic acids was done using Potyvirus universal primer and DNA sequencing. Disease incidence in Bangli, Buleleng, and Denpasar Regencies was > 50%. RT-PCR and CiFor/CiRev Potyvirus universal primers successfully amplified ± 700 bp of CI genes from all samples from Bangli, while samples from 8 other districts were not amplified using the same primers. The SPVC isolate of sweet potato showed nucleotide and amino acid homology similarities with the sweet potato isolate from East Timor (MF572066), 96.8% and 97.4%, respectively and these were referred to the "Asian" strain. This indicates that SPVC has spread in East Java and Bali.

An Issue of Concern: Unique Truncated ORF8 Protein Variants of SARS-CoV-2

Open reading frame 8 (ORF8) protein is one of the most evolving accessory proteins in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits presentation of viral antigens by the major histocompatibility complex class I (MHC-I) and interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 to evade immunity and replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein defines the B.1.1.7 lineage of SARS-CoV-2, which is engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) due to the Q27STOP mutations were identified among 49055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents which includes Africa, Asia, Europe and South America. Based on various quantitative features such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, a collection of nine possible T-ORF8 unique variants were defined. The question of whether T-ORF8 variants work similarly to ORF8 has yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.

Metagenomic Identification of a New Sarbecovirus from Horseshoe Bats in Europe

The source of the COVID-19 pandemic is unknown, but the natural host of the progenitor sarbecovirus is thought to be Asian horseshoe (rhinolophid) bats. We identified and sequenced a novel sarbecovirus (RhGB01) from a British horseshoe bat, at the western extreme of the rhinolophid range. Our results extend both the geographic and species ranges of sarbecoviruses and suggest their presence throughout the horseshoe bat distribution. Within the receptor binding domain, but excluding the receptor binding motif, RhGB01 has a 77% (SARS-CoV-2) and 81% (SARS-CoV) amino acid homology. While apparently lacking hACE2 binding ability, and hence unlikely to be zoonotic without mutation, RhGB01 presents opportunity for SARS-CoV-2 and other sarbecovirus homologous recombination. Our findings highlight that the natural distribution of sarbecoviruses and opportunities for recombination through intermediate host co-infection are underestimated. Preventing transmission of SARS-CoV-2 to bats is critical with the current global mass vaccination campaign against this virus.

Abundant transmission of Corona Virus Nsp2 RNA Topoisomerse I120F Mutants with Concurrence D614G Spike Protein Mutation in Australia

We previously predicted Nsp2 Corona virus protein as RNA topoisomerase through amino acid homology among Vibrio haemolytica DNA topoisomerase IA/IV as well as DNA primase, DNA gyrase and bi-subunit Trypanosoma brucei DNA topoisomerase IB. Many DNA topoisomerase I/III have RNA topoisomerase activity and such ubiquitous enzymes are conserved and involved in the regulation of replication and transcription. We have checked here mutational profile of Nsp2 RNA topoisomerase analyzing >10000 orf1a 4405 amino acid length Corona virus polyprotein. Mutant proteins were selected by BLAST search having 99.84% sequence similarity and 181-818aa portion Nsp2 protein (protein id. QIU82057) was analyzed using CLUSTAL Omega software. We found 26 different mutations where most changes were selected at Isoleucine and Alanine into Valine or Leucine into Phenylanaline pinpointing conserved nature of the Corona virus RNA topoisomerase. Major nonsense very abundant mutations were found at I120F (Isoleucine to Phenylalanine). Other important mutations were R27C, I198V, T85I, L410F, I559V and P583S. The I120F mutation was abundant in Australian isolates and its spread was seen in the Bangladesh and other countries like USA. We suggest that abundant I120F mutation of Nsp2 Topoisomerase may increase transmission of Corona virus by stabilizing RNA structure for efficient virus pakaging. Interestingly, such mutations were found in association of D614G mutation of Spike protein, known to >70% increase infectivity. On the contrary, all P583S Nsp2 mutants analyzed had no concurrence D614G spike protein mutation. Many silent mutations (5-7) were detected by genome wide analysis but no N501Y Spike protein mutation. This is first report that predicts a link of greater Corona virus transmission with Nsp2 protein I120F and spike protein D614G mutations.

An updated overview on 2019 novel coronavirus

Coronavirus (CoV) has been associated with several infectious disease outbreak in humans in the past two decades, including Severe respiratory syndrome coronavirus [SARS-CoV] in 2002-2003 and Middle East respiratory coronavirus [MERS-CoV] in 2012. An unexpected and unexplained respiratory infection commenced at Wuhan city, China, during the end of 2019, which was named as novel coronavirus disease [2019-nCoV or COVID-19] by the World Health Organization (WHO). It is considered to be a zoonotic disease, as it has nearly similar amino acid homology to SARS-CoV. Reports have revealed an unexpected increase in number of cases worldwide (214 countries and territories along with 2 international conveyances), which intimidates the public with human to human escalation through respiratory droplets and contact routes. This pandemic was declared as a public health emergency of international concern. It follows an extremely heterogeneous course from mild Flu like symptoms [fever, cough, sore throat, dyspnoea, fatigue, headache and malaise] to severe acute respiratory distress syndrome. According to epidemiological data, old age and pre-existing medical co-morbidities are considered to be the risk factors for COVIOD-19. Currently, laboratory-based "Real time-reversed transcription Polymerase chain reaction" [rtRT-PCR] remains the molecular test of choice for the etiologic diagnosis. That apart, several hematological, biochemical markers along with various inflammatory cytokines (lymphopenia, serum level of C-reactive protein, D-dimer, ferritin, Interleukin-6, cardiac troponin I) may be used to assess disease severity. As of now, there have been approximately more than 36 million cases worldwide and more than one million succumbed to the illness (2.91% estimated mortality rate). Based on reports, India has become the second worst coronavirus hit country with a total number of cases reaching 68 lakhs. The dearth of selected medication (anti-CoV) and unusual transmission ability of 2019-nCoV continue to be responsible for this uninterrupted escalation. Woefully, specific vaccines are yet to come up. Treatment options like broad-spectrum antiviral Remdesivir, and oxygen therapy are being evaluated to control this unprecedented health crisis, although none of these drugs are FDA (Food and drug administration) approved. The path of this pandemic is very undetermined and unpredictable. In the present scenario, efficacious prevention needs swift action from the standpoint of public health strategies, which entails strict surveillance, rapid detection, and implementation of a containment plan to curb this outbreak. This review article highlights the updates on novel coronavirus 2019 and the uninterrupted apocalyptic progress concerning the present situation. It also highlights various perspectives of effective therapeutic strategies to restrain this viral outbreak.

Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2

ABSTRACTThe global public health is endangered due to COVID-19 pandemic, which is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Despite having similar pathology to MERS and SARS-CoV, the infection fatality rate of SARS-CoV-2 is likely lower than 1%. SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. Some of these mutations decrease the stability of ORF10, e.g. I4L and V6I were found in the MoRF region of ORF10 which may also possibly contribute to Intrinsic protein disorder. Furthermore, a physicochemical and structural comparative analysis was carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid homology. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Altogether, SARS-CoV-2 ORF10 is a promising pharmaceutical target and a protein which should be monitored for changes which correlate to change pathogenesis and clinical course of COVID-19 infection.

Molecular characteristics of the VP1 region of enterovirus 71 strains in China

Background: Enterovirus 71 (EV71) is the most commonly implicated causative agent of severe outbreaks of paediatric hand, foot, and mouth disease (HFMD).VP1 protein, a capsid protein of EV71, is responsible for the genotype of the virus and is essential for vaccine development and effectiveness. However, the genotypes of EV71 isolates in China are still not completely clear.Methods: The VP1 gene sequences of 3712 EV71 virus strains from China,excluding repetitive sequences and 30 known EV71 genotypes as reference strains, between 1986 and 2019 were obtained from GenBank. Phylogenetic tree, amino acid homology, genetic variation and genotype analyses of the EV71VP1 protein were performed with MEGA 6.0 software.Results: The amino acid identity was found to be 88.33%~100% among the 3712 EV71 strains, 93.47%~100% compared with vaccine strain H07, and 93.04%~100% compared with vaccine strains FY7VP5 or FY-23K-B. Since 2000, the prevalent strains of EV71 were mainly of the C4 genotype. Among these, the C4a subgenotype was predominant, followed by the C4b subgenotype; other subgenotypes appeared sporadically between 2005 and 2018 in mainland China. The B4 genotype was the main genotype in Taiwan, and the epidemic strains were constantly changing. Some amino acid variations in VP1 of EV71 occurred with high frequencies, including A289T (20.99%), H22Q (16.49%), A293S (15.95%), S283T (15.11%), V249I (7.76%), N31D (7.25%), and E98K (6.65%).Conclusion: The C4 genotype of EV71 in China matches the vaccine and should effectively control EV71. However, the efficacy of the vaccine is partially affected by the continuous change in epidemic strains in Taiwan. These results suggest that the genetic characteristics of the EV71-VP1 region should be continuously monitored, which is critical for epidemic control and vaccine design to prevent EV71 infection in children.