The prevalence,origin, and prevention of six human coronaviruses

正CORONAVIRUSES Coronaviruses(CoVs)are a large group of viruses found in many species of animals around the world,particularly bats and wild birds.CoVs result in various clinical manifestations ranging from asymptomatic respiratory,hepatic,and enteric     

Bat origin of a new human coronavirus: there and back again

Science China Life Sciences -     

Erratum to: Bat origin of a new human coronavirus: there and back again

正We miscalculated identities of several genes, and the corrected Table 1 should be as follows:a) This table demonstrates identities of 2019-nCoV WIV04 (GenBank Accession No. MN996528.1) compared with bat SARSr-CoV RaTG13 (GenBank Accession No. MN996532.1) and SARS-CoV BJ01 (GenBank Accession No. AY278488.2). Identities were calculated by using nucleotide sequences and     

Comparative genomic signature representations of the emerging COVID-19 coronavirus and other coronaviruses: High identity and possible recombination between Bat and Pangolin coronaviruses

Coronaviruses are responsible on respiratory diseases in animal and human. The combination of numerical encoding techniques and digital signal processing methods are becoming increasingly important in handling large genomic data. In this paper, we propose to analyze the SARS-CoV-2 genomic signature using the combination of different nucleotide representations and signal processing tools in the aim to identify its genetic origin. The sequence of SARS-CoV-2 was compared with 21 relevant sequences including Bat, Yak and Pangolin coronavirus sequences. In addition, we developed a new algorithm to locate the nucleotide modifications. The results show that the Bat and Pangolin coronaviruses were the most related to SARS-CoV-2 with 96% and 86% of identity all along the genome. Within the S gene sequence, the Pangolin sequence presents local highest nucleotide identity. Those findings suggest genesis of SARS-Cov-2 through evolution from Bat and Pangolin strains. This study offers new ways to automatically characterize viruses.     

Global landscape of patents related to human coronaviruses

At present, the COVID-19 pandemic is running rampant, having caused 2.18 million deaths. Characterizing the global patent landscape of coronaviruses is essential not only for informing research and policy, given the current pandemic crisis, but also for anticipating important future developments. While patents are a promising indicator of technological knowledge production widely used in innovation research, they are often an underused resource in biological sciences. In this study, we present a patent landscape for the seven coronaviruses known to infect humans. The information included in this paper provides a strong intellectual groundwork for the ongoing development of therapeutic agents and vaccines along with a deeper discussion of intellectual property rights under epidemic conditions. The results show that there has been a rapid increase in human coronavirus patents, especially COVID-19 patents. China and the United States play an outstanding role in global cooperation and patent application. The leading role of academic institutions and government is increasingly apparent. Notable technological issues related to human coronaviruses include pharmacochemical treatment, diagnosis of viral infection, viral-vector vaccines, and traditional Chinese medicine. Furthermore, a critical challenge lies in balancing commercial competition, enterprise profit, knowledge sharing, and public interest.     

Replication of enterotropic and polytropic murine coronaviruses in cultured cell lines of mouse origin.

To understand the virus-cell interactions that occur during murine coronavirus infection, six murine cell lines (A3-1M, B16, CMT-93, DBT, IC-21 and J774A.1) were inoculated with eight murine coronaviruses, including prototype strains of both polytropic and enterotropic biotypes, and new isolates. All virus strains produced a cytopathic effect (CPE) with cell-to-cell fusion in B16, DBT, IC-21 and J774A.1 cells. The CPE was induced most rapidly in IC-21 cells and was visible microscopically in all cell lines tested. In contrast, the coronaviruses produced little CPE in A3-1M and CMT-93 cells. Although most virus-infected cells, except KQ3E-infected A3-1M, CMT-93 and J774A.1 cells, produced progeny viruses in the supernatants when assayed by plaque formation on DBT cells, the kinetics of viral replication were dependent on both the cell line and virus strain; replication of prototype strains was higher than that of new isolates. There was no significant difference in replication of enterotropic and polytropic strains. B16 cells supported the highest level of viral replication. To determine the sensitivity of the cell lines to murine coronaviruses, the 50% tissue culture infectious dose of the coronaviruses was determined with B16, DBT, IC-21 and J774A.1 cells, and compared to that with DBT cells. The results indicate that IC-21 cells were the most sensitive to murine coronaviruses. These data suggest that B16 and IC-21 cells are suitable for large-scale preparation and isolation of murine coronaviruses, respectively.     

Prevalence and genetic diversity analysis of human coronaviruses among cross-border children

Background

More than a decade after the outbreak of human coronaviruses (HCoVs) SARS in Guangdong province and Hong Kong SAR of China in 2002, there is still no reoccurrence, but the evolution and recombination of the coronaviruses in this region are still unknown. Therefore, surveillance on the prevalence and the virus variation of HCoVs circulation in this region is conducted.

Methods

A total of 3298 nasopharyngeal swabs samples were collected from cross-border children (<6 years, crossing border between Southern China and Hong Kong SAR) showing symptoms of respiratory tract infection, such as fever (body temperature?>?37.5 °C), from 2014 May to 2015 Dec. Viral nucleic acids were analyzed and sequenced to study the prevalence and genetic diversity of the four human coronaviruses. The statistical significance of the data was evaluated with Fisher chi-square test.

Results

78 (2.37%; 95%CI 1.8-2.8%) out of 3298 nasopharyngeal swabs specimens were found to be positive for OC43 (36;1.09%), HKU1 (34; 1.03%), NL63 (6; 0.18%) and 229E (2;0.01%). None of SARS or MERS was detected. The HCoVs predominant circulating season was in transition of winter to spring, especially January and February and NL63 detected only in summer and fall. Complex population with an abundant genetic diversity of coronaviruses was circulating and they shared homology with the published strains (99-100%). Besides, phylogenetic evolutionary analysis indicated that OC43 coronaviruses were clustered into three clades (B,D,E), HKU1 clustered into two clades(A,B) and NL63 clustered into two clades(A,B). Moreover, several novel mutations including nucleotides substitution and the insertion of spike of the glycoprotein on the viral surface were discovered.

Conclusions

The detection rate and epidemic trend of coronaviruses were stable and no obvious fluctuations were found. The detected coronaviruses shared a conserved gene sequences in S and RdRp. However, mutants of the epidemic strains were detected, suggesting continuous monitoring of the human coronaviruses is in need among cross-border children, who are more likely to get infected and transmit the viruses across the border easily, in addition to the general public.

     

Translational control of coronaviruses

Coronaviruses represent a large family of enveloped RNA viruses that infect a large spectrum of animals. In humans, the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic and is genetically related to SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), which caused outbreaks in 2002 and 2012, respectively. All viruses described to date entirely rely on the protein synthesis machinery of the host cells to produce proteins required for their replication and spread. As such, virus often need to control the cellular translational apparatus to avoid the first line of the cellular defense intended to limit the viral propagation. Thus, coronaviruses have developed remarkable strategies to hijack the host translational machinery in order to favor viral protein production. In this review, we will describe some of these strategies and will highlight the role of viral proteins and RNAs in this process.     

Two-tube multiplex real-time reverse transcription PCR to detect six human coronaviruses

正Dear Editor,Coronaviruses are enveloped positive-strand RNA viruses with 27–33 kb genomes.These viruses are classified into four genera,namely Alphacoronavirus,Betacoronavirus,Gammacoronavirus,and Deltacoronavirus     

拇指大小的蝙蝠

扁颅蝠是继凹脸蝠之后的世界第二小蝙蝠，褐扁颅蝠与扁颅蝠同在一个属，扁颅蝠属就只有这两个种，世界最小的凹脸蝠体重仅为2克左右，扁颅蝠也下过3.5克左右。褐扁颅蝠也就4．3克左右，虽然打开翼膜后看起来比较大，但是它们的身体并不比我们成年人的拇指大。     

FASN inhibitor TVB-3166 prevents S-acylation of the spike protein of human coronaviruses

The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other coronaviruses mediates host cell entry and is S-acylated on multiple phylogenetically conserved cysteine residues. Multiple protein acyltransferase enzymes have been reported to post-translationally modify spike proteins; however, strategies to exploit this modification are lacking. Using resin-assisted capture MS, we demonstrate that the spike protein is S-acylated in SARS-CoV-2-infected human and monkey epithelial cells. We further show that increased abundance of the acyltransferase ZDHHC5 associates with increased S-acylation of the spike protein, whereas ZDHHC5 knockout cells had a 40% reduction in the incorporation of an alkynyl-palmitate using click chemistry detection. We also found that the S-acylation of the spike protein is not limited to palmitate, as clickable versions of myristate and stearate were also labelled the protein. Yet, we observed that ZDHHC5 was only modified when incubated with alkyne-palmitate, suggesting it has specificity for this acyl-CoA, and that other ZDHHC enzymes may use additional fatty acids to modify the spike protein. Since multiple ZDHHC isoforms may modify the spike protein, we also examined the ability of the FASN inhibitor TVB-3166 to prevent S-acylation of the spike proteins of SARS-CoV-2 and human CoV-229E. We show that treating cells with TVB-3166 inhibited S-acylation of expressed spike proteins and attenuated the ability of SARS-CoV-2 and human CoV-229E to spread in vitro. Our findings further substantiate the necessity of CoV spike protein S-acylation and demonstrate that de novo fatty acid synthesis is critical for the proper S-acylation of the spike protein.     

Infection of primary cultures of human neural cells by human coronaviruses 229E and OC43.

We evaluated the ability of human coronaviruses to infect primary cultures of human neural cells. Double immunofluorescence with antibodies to virus and cell markers showed infection of fetal astrocytes and of adult microglia and astrocytes by strain OC43. RNA amplification revealed infection of fetal astrocytes, adult microglia, and a mixed culture of adult oligodendrocytes and astrocytes by strain 229E. Infectious virus was released only from fetal astrocytes, with higher titers for OC43. Human coronaviruses have the capacity to infect some cells of the central nervous system, although infection of adult cells appears abortive.     

Broad strategies for neutralizing SARS-CoV-2 and other human coronaviruses with monoclonal antibodies

Antibody therapeutics and vaccines for coronavirus disease 2019(COVID-19) have been approved in many countries, with most being developed based on the original strain of severe acute respiratory syndrome coronavirus 2(SARS-Co V-2). SARS-Co V-2has an exceptional ability to mutate under the pressure of host immunity, especially the immune-dominant spike protein of the virus, which is the target of both antibody drugs and vaccines. Given the continuous evolution of the virus and the identification ...