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Journal: Journal of virology


On January 26 2020, the first Coronavirus Disease 2019 (COVID-19) case was reported in Arizona (3rd case in the US) (1).….


Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen [lsqb]HLA[rsqb] A, B, and C) may affect susceptibility to and severity of severe acute respiratory syndrome 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19). We execute a comprehensive in silico analysis of viral peptide-MHC class I binding affinity across 145 HLA -A, -B, and -C genotypes for all SARS-CoV-2 peptides. We further explore the potential for cross-protective immunity conferred by prior exposure to four common human coronaviruses. The SARS-CoV-2 proteome is successfully sampled and presented by a diversity of HLA alleles. However, we found that HLA-B*46:01 had the fewest predicted binding peptides for SARS-CoV-2, suggesting individuals with this allele may be particularly vulnerable to COVID-19, as they were previously shown to be for SARS (Lin M, Tseng H-K, Trejaut JA, Lee H-L, Loo J-H, Chu C-C, Chen P-J, Su Y-W, Lim KH, Tsai Z-U, Lin R-Y, Lin R-S, Huang C-H. BMC Med Genet 4:9. 2003.). Conversely, we found that HLA-B*15:03 showed the greatest capacity to present highly conserved SARS-CoV-2 peptides that are shared among common human coronaviruses, suggesting it could enable cross-protective T-cell based immunity. Finally, we report global distributions of HLA types with potential epidemiological ramifications in the setting of the current pandemic.IMPORTANCE Individual genetic variation may help to explain different immune responses to a virus across a population. In particular, understanding how variation in HLA may affect the course of COVID-19 could help identify individuals at higher risk from the disease. HLA typing can be fast and inexpensive. Pairing HLA typing with COVID-19 testing where feasible could improve assessment of viral severity in the population. Following the development of a vaccine against SARS-CoV-2, the virus that causes COVID-19, individuals with high-risk HLA types could be prioritized for vaccination.


There are seven antigenically distinct serotypes of foot-and-mouth disease virus (FMDV), each of which has intra-typic variants. In the present study, we have developed methods to efficiently generate promising vaccines against seven serotypes or subtypes. The capsid-coding gene (P1) of the vaccine strain O1/Manisa/Turkey/69 was replaced with the amplified or synthetic genes from the O, A, Asia1, C, SAT 1, SAT 2, and SAT 3 serotypes. The seven serotype viruses were rescued successfully. Each chimeric FMDV with replacing P1 showed its serotype-specific antigenicity and varied in terms of pathogenesis in pigs and mice. Pigs vaccinated with an experimental trivalent vaccine containing the inactivated recombinants based on the main serotypes O, A, and Asia1 effectively protected them from virus challenge. This technology could be a potential strategy for customized vaccine with challenge tool to protect against epizootic disease from specific serotypes or subtypes of FMDV.IMPORTANCE Foot-and-mouth disease virus (FMDV) causes significant economic losses. For the vaccine preparation, the selection of vaccine strains was complicated by its high antigenic variation. In the present study, we suggested that an effective strategy can be rapidly prepare and evaluate a mass-producing customized vaccines against epidemic strains. The P1 gene encoding the structural proteins of the well-known vaccine virus was replaced by the synthetic or amplified genes of seven representative serotype viruses. These chimeric viruses generally replicated readily in cell culture and had the similar particle size as the original vaccine strain. Their antigenicity mirrored that of the original serotype from which their P1 gene was derived. Animal infection experiments revealed that the recombinants varied in terms of pathogenicity. This strategy will be a useful tool for rapidly generating customized FMD vaccines or challenge viruses against all serotypes, especially for FMD-free countries which have prohibited import of FMDVs.

Concepts: Immune system, Microbiology, Virus, Vaccine, Vaccination, Influenza, Aphthovirus, Foot-and-mouth disease


The foot-and-mouth disease virus (FMDV) afflicts livestock in more than 80 countries limiting food production and global trade. Production of foot-and-mouth disease (FMD) vaccines requires cytosolic expression of the FMDV 3C protease to cleave the P1 polyprotein into mature capsid proteins, but the FMDV 3C protease is toxic to host cells. To identify less toxic isoforms of the FMDV 3C protease, we screened 3C mutants for increased transgene output over wild-type 3C using a Gaussia luciferase reporter system. The novel point-mutation 3C(L127P) increased yields of recombinant FMDV subunit proteins in mammalian and bacterial cells expressing P1-3C transgenes and retained the ability to process P1 polyproteins from multiple FMDV serotypes. The 3C(L127P) mutant produced crystalline-arrays of FMDV virus-like particles in mammalian and bacterial cells, potentially providing a practical method of rapid, inexpensive FMD vaccine production in bacteria.Importance: The mutant FMDV 3C protease L127P significantly increased yields of recombinant FMDV subunit antigens and produced virus-like particles in mammalian and bacterial cells. The L127P mutation provides a novel advancement for economical FMD vaccine production.

Concepts: DNA, Protein, Gene, Bacteria, Microbiology, Virology, Aphthovirus, Foot-and-mouth disease


Chikungunya virus (CHIKV), a mosquito-borne human pathogen, causes a disabling disease characterized by severe joint pain that can persist for weeks, months or even years in patients. The non-structural protein 3 (nsP3) plays essential roles during acute infection, but little is known about the function of nsP3 during chronic disease. Here, we used sub-diffraction multi-color microscopy for spatial and temporal analysis of CHIKV nsP3 within human cells that persistently replicate replicon RNA. Round cytoplasmic granules of various sizes (i) contained nsP3 and stress granule assembly factors 1 and 2 (G3BP1/2); (ii) were next to double-stranded RNA foci and nsP1-positive structures; and (iii) were close to the nuclear membrane and the nuclear pore complex protein Nup98. Analysis of protein turnover and mobility by live-cell microscopy revealed that granules could persist for hours to days, accumulated newly synthesized protein, and moved through the cytoplasm at varying speeds. Granules also had a static internal architecture and were stable in cell lysates. Refractory cells that had cleared the non-cytotoxic replicon regained the ability to respond to arsenite-induced stress. In summary, nsP3 can form uniquely stable granular structures that persist long-term within the host cell. This continued presence of viral and cellular protein-complexes has implications for the study of the pathogenic consequences of lingering CHIKV infection and the development of strategies to mitigate the burden of chronic musculoskeletal disease brought about by a medically important arthropod-borne virus (arbovirus).ImportanceChikungunya virus (CHIKV) is a re-emerging alphavirus transmitted by mosquitos and causes transient sickness but also chronic disease affecting muscles and joints. No approved vaccines or antivirals are available. Thus, a better understanding of the viral life cycle and the role of viral proteins can aid in identifying new therapeutic targets. Advances in microscopy and development of non-cytotoxic replicons (Utt, Das, Varjak, Lulla, Lulla, Merits, J Virol 89:3145-62, 2015, doi:10.1128/JVI.03213-14) have allowed researchers to study viral proteins within controlled laboratory environments over extended durations. Here we established human cells that stably replicate replicon RNA and express tagged non-structural protein 3. The ability to track nsP3 within the host cell and during persistent replication can benefit fundamental research efforts to better understand long-term consequences of the persistence of viral protein complexes and thereby provide the foundation for new therapeutic targets to control CHIKV infection and treat chronic disease symptoms.


Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) has a narrow host cell tropism, limited to cells of the monocyte/macrophage lineage. CD163 protein is expressed at high levels on the surface of specific macrophage types and a soluble form is circulating in blood. CD163 has been described as a fusion receptor for PRRSV, with the scavenger receptor cysteine-rich domain 5 (SRCR5) region having been shown to be the interaction site for the virus.As reported earlier, we have generated pigs in which Exon 7 of the CD163 gene has been deleted using CRISPR/Cas9 editing in pig zygotes. These pigs express CD163 protein lacking SRCR5 (ΔSRCR5 CD163) and show no adverse effects when maintained under standard husbandry conditions. The ΔSRCR5 CD163 was not only detected on the surface of macrophage subsets, but the secreted, soluble protein can also detected in the serum of the edited pigs, as shown here by porcine soluble CD163-specific ELISA. Previous results showed that primary macrophage cells from ΔSRCR5 CD163 animals are resistant to PRRSV-1, subtypes 1, 2, and 3, as well as PRRSV-2 infection in vitro Here, ΔSRCR5 pigs were challenged with a highly virulent PRRSV-1, subtype 2 strain. In contrast to the wildtype control group, ΔSRCR5 pigs showed no signs of infection and no viremia or antibody response indicative of a productive infection. Histopathological analysis of lung and lymph node tissue showed no presence of virus replicating cells in either tissue. This shows that ΔSRCR5 pigs are fully resistant to infection by the virus.Importance Porcine Reproductive and Respiratory Syndrome virus (PRRSV) is the etiological agent of PRRS, causing late-term abortions, stillbirths, and respiratory disease in pigs, incurring major economic losses to the world-wide pig industry. The virus is highly mutagenic and can be divided into two species, PRRSV-1 and PRRSV-2, each containing several subtypes. Current control strategies mainly involve biosecurity measures, depopulation, and vaccination. Vaccines are at best only partially protective against infection with heterologous subtypes and sublineages and modified-live vaccines have frequently been reported to revert to virulence. Here we demonstrate that a genetic control approach results in complete resistance to PRRSV infection in vivo CD163 is edited such as to remove the viral interaction domain while maintaining protein expression and biological function, averting any potential adverse effect associated with protein knock-out. This research demonstrates a genetic control approach with potential benefits in animal welfare as well as to the pork industry.


Recent discoveries of new large DNA viruses reveal high diversity in their morphologies, genetic repertoires, and replication strategies. Here, we report the novel features of Medusavirus, a large DNA virus newly isolated from hot spring water in Japan. Medusavirus with a diameter of 260 nm shows a T=277 icosahedral capsid with unique spherical-headed spikes on its surface. It has a 381 kb genome encoding 461 putative proteins, 86 of which have their closest homologs in Acanthamoeba castellanii, whereas 279 (61%) are ORFans. The virus lacking the genes of DNA topoisomerase II and RNA polymerase showed that the DNA replication takes place in the host nucleus while the progeny virions are assembled in the cytoplasm. Furthermore, Medusavirus encoded all of five types of histones (H1, H2A, H2B, H3, and H4) and one DNA polymerase, which are phylogenetically placed at the root of the eukaryotic clades. By contrast, the host amoeba encoded many Medusavirus homologs including the major capsid protein. These facts strongly suggested that amoeba is indeed the most promising natural host of Medusavirus, and lateral gene transfers have taken place repeatedly and bidirectionally between the virus and its host since the early stage of their co-evolution. Medusavirus reflects the traces of direct evolutionary interactions between the virus and eukaryotic hosts, which may be caused by sharing the DNA replication compartment and evolutionarily long lasting viral-host relationships. Based on its unique morphological characteristics and phylogenomic relationships with other known large DNA viruses, we propose that Medusavirus forms a new family MedusaviridaeIMPORTANCE We have isolated a new NCLDV virus from hot spring water in Japan, named Medusavirus. This new NCLDV is phylogenetically placed at the root of the eukaryotic clades based on the phylogenies of several key genes including DNA polymerase, and surprisingly encodes the full set of histone homologs. Furthermore, its laboratory host, Acanthamoeba castellanii, encodes many Medusavirus homologs in its genome including the major capsid protein, suggesting that the amoeba is the genuine natural host of this new virus from ancient times, and lateral gene transfers have occurred between the virus and amoeba repeatedly. These results suggest that Medusavirus is a unique NCLDV preserving ancient footprints of evolutionary interactions with its hosts, thus providing clues to elucidate the evolution of NCLDVs, eukaryotes, and viral-host interaction. Based on the dissimilarities with other known NCLDVs, we propose that Medusavirus forms a new viral family Medusaviridae.


The rise of populist movements worldwide is challenging science and motivating scientists to join the debate and enter politics. Based on my experience, taking a public stand will not come without slanderous personal and institutional attacks as an attempt to shake scientific credibility. The virology community is at risk of similar misrepresentation; reflection on this topic, and particularly on how to address such challenges, should be a priority, given we are in the “post-truth” era.


Poliomyelitis is a highly infectious disease caused by poliovirus (PV). It can result in paralysis and may be fatal. Integrated global immunisation programmes using live-attenuated oral (OPV) and/or inactivated PV vaccines (IPV) have systematically reduced its spread and paved the way for eradication. Immunisation will continue post-eradication to ensure against reintroduction of the disease, but there are biosafety concerns for both OPV and IPV. These could be addressed by the production and use of virus-free virus-like particle (VLP) vaccines which mimic the ‘empty’ capsids (ECs) normally produced in viral infection. Although ECs are antigenically indistinguishable from mature virus particles, they are less stable and readily convert to an alternative conformation unsuitable for vaccine purposes. Stabilised ECs, expressed recombinantly as VLPs, could be ideal candidate vaccines for a polio-free world. However, although genome-free PV ECs have been expressed as VLPs in a variety of systems, their inherent antigenic instability has proved a barrier to further development. In this study, we have selected thermally-stable ECs of type-1 PV (PV-1). The ECs are antigenically stable at temperatures above the conversion temperature of wild type (wt) virion. We have identified mutations on the capsid surface and internal networks that are responsible for the EC stability. With reference to the capsid structure, we speculate on the roles of these residues in capsid stability and postulate that such stabilised VLPs could be used as novel vaccines.

Concepts: Immune system, Infectious disease, Microbiology, Vaccine, Vaccination, Infection, Polio vaccine, Virus-like particle


During the summer of 2012, in Jeddah, Saudi Arabia a hitherto unknown coronavirus was isolated from the sputum of a patient with acute pneumonia and renal failure (1, 2).…

Concepts: Saudi Arabia, Arabian Peninsula, Riyadh, United Arab Emirates, Middle East, Qatar, Jordan, Arabic language