Highlights d SARS-CoV-2 nucleocapsid mutations R203K/G204R associate with B.1.1.7 (Alpha) emergence d R203K/G204R variants possess a replication advantage over the preceding lineages d R203K/G204R variants show enhanced infectivity and disease severity in the hamster model

To trace the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), we collected and thoroughly analyzed 29,452 publicly available coronavirus genomes, including 26,312 genomes of SARS-CoV-2 strains. We observed coronavirus recombination events among different hosts including 3 independent recombination events with statistical significance between some isolates from humans, bats and pangolins. Consistent with previous records, we also detected putative recombination between strains similar or related to Bat-CoV-RaTG13 and Pangolin-CoV-2019. The putative recombination region is located inside the receptor-binding domain (RBD) of the spike glycoprotein (S protein), which may represent the origin of SARS-CoV-2. Population genetic analyses provide estimates suggesting that the putative introduced DNA within the RBD is undergoing directional evolution. This may result in the adaptation of the virus to hosts. Unsurprisingly, we found that the putative recombination region in S protein was highly diverse among strains from bats. Bats harbor numerous coronavirus subclades that frequently participate in recombination events with human coronavirus. Therefore, bats may provide a pool of genetic diversity for the origin of SARS-CoV-2.

The novel coronavirus (SARS-CoV-2) has become a pandemic and is threatening human health globally. Here, we report 9 newly evolved SARS-CoV-2 single nucleotide polymorphism (SNP) alleles those underwent a rapid increase (7 cases) or decrease (2 cases) in their frequency for 30% ∼ 80% in the initial four months, which are further confirmed by intra-host single nucleotide variation (iSNV) analysis using raw sequence data including 8217 samples. The 9 SNPs are mostly (8/9) located in the coding region and are mainly (6/9) nonsynonymous substitutions. The 9 SNPs show a complete linkage in SNP pairs and belong to 3 different linkage groups, named LG_1 to LG_3. Analyses in population genetics show signatures of adaptive selection towards the mutants in LG_1, but no signal of selection for LG_2. Population genetic analysis results on LG_3 show geological differentiation. Analyses on geographic COVID-19 cases and published clinical data provide evidence that the mutants in LG_1 and LG_3 benefit virus replication and those in LG_1 have a positive correlation with the disease severity in COVID-19 infected patients. The mutants in LG_2 show a bias towards mildness of the disease based on available public clinical data. Our findings may be instructive for epidemiological surveys and disease control of COVID-19 in the future.

In addition to the mutations on the spike protein (S), co-occurring mutations on nucleocapsid (N) protein are also emerging in SARS-CoV-2 world widely. Mutations R203K/G204R on N, carried by high transmissibility SARS-CoV-2 lineages including B.1.1.7 and P.1, has a rapid spread in the pandemic during the past year. In this study, we performed comprehensive population genomic analyses and virology experiment concerning on the evolution, causation and virology consequence of R203K/G204R mutations. The global incidence frequency (IF) of 203K/204R has rose up from nearly zero to 76% to date with a shrinking from August to November in 2020 but bounced later. Our results show that the emergence of B.1.1.7 is associated with the second growth of R203K/G204R mutants. We identified positive selection evidences that support the adaptiveness of 203K/204R variants. The R203K/G204R mutant virus was created and compared with the native virus. The virus competition experiments show that 203K/204R variants possess a replication advantage over the preceding R203/G204 variants, possibly in relation to the ribonucleocapsid (RNP) assemble during the virus replication. Moreover, the 203K/204R virus increased the infectivity in a human lung cell line and induced an enhanced damage to blood vessel of infected hamsters' lungs. In consistence, we observed a positive association between the increased severity of COVID-19 and the IF of 203K/204R from in silicon analysis of global clinical and epidemic data. In combination with the informatics and virology experiment, our work suggested the contribution of 203K/204R to the increased transmission and virulence of the SARS-CoV-2. In addition to mutations on the S protein, the mutations on the N protein are also important to virus spread during the pandemic.

Senecavirus A (SVA), an emerging picornavirus in porcine population, could infect porcines of all age group and cause FMD-like symptoms. Picornaviridae, a group of RNA viruses do harm to both human and stocks; however, most of picornaviruses are lack of effective vaccines and drugs. Picornaviral 3C protease (3C pro ), as an important role in virus maturation, they basically take charge of poly-protein cleavaging, RNA replication, and multiple interventions on host cells. In this study, we successfully solved the crystal structure of 3C pro at 1.9 Å resolution. The results showed several differences of the binding groove within picornaviral 3C pro , and prompted that the accommodate ability of the pocket may associate with the cleavage efficiency. The further research on 3C pro cleavage efficiency based on structural biology, will prospectively provide an instruction on designing of efficient 3C pro for universally proteolysis in picornaviral VLP production.

The recent outbreak of COVID-19 caused by a new zoonotic origin coronavirus (SARS-CoV-2 or 2019-nCoV) has sound the alarm for the potential spread of epidemic coronavirus crossing species. With the urgent needs to assist disease control and to provide invaluable scientific information, we developed the coronavirus database (CoVdb), an online genomic, proteomic and evolutionary analysis platform. CoVdb has brought together genomes of more than 5000 coronavirus strains, which were collected from 1941 to 2020, in more than 60 countries and in hosts belonging to more than 30 species, ranging from fish to human. CoVdb presents comprehensive genomic information, such as gene function, subcellular localization, topology and protein structure. To facilitate coronavirus research, CoVdb also provides flexible search approaches and online tools to view and analyze protein structure, to perform multiple alignments, to automatically build phylogenetic trees and to carry on evolutionary analyses. CoVdb can be accessed freely at http://covdb.popgenetics.net. Hopefully, it will accelerate the progress to develop medicines or vaccines to control the pandemic of COVID-19.

No abstract

African swine fever is a widespread and highly contagious disease in the porcine population, which is caused by African swine fever virus (ASFV). The PCR and ELISA detection methods are the main conventional diagnostic methods for ASFV antigen/antibody detection in the field. However, these methods have limitations of expensive equipment, trained technicians, and time-consuming results. Thus, a rapid, inexpensive, accurate and on-site detection method is urgently needed. Here we describe a double-antigen-sandwich lateral-flow assay based on gold nanoparticle-conjugated ASFV major capsid protein p72, which can detect ASFV antibody in serum samples with high sensitivity and specificity in 10 min and the results can be determined by naked eyes. A lateral flow assay was established by using yeast-expressed and acid-treated ASFV p72 conjugated with gold nanoparticles, which are synthesized by seeding method. A high coincidence (97.8%) of the assay was determined using clinical serum compared to a commercial ELISA kit. In addition, our lateral flow strip can detect as far as 1:10,000 diluted clinically positive serum for demonstration of high sensitivity. In summary, the assay developed here was shown to be rapid, inexpensive, accurate and highly selective. It represents a reliable method for on-site ASFV antibody detection and may help to control the ASFV pandemic.