In vivo structure and dynamics of the RNA genome of SARS-Cov-2

The SARS-CoV-2 coronavirus, which causes the COVID-19 pandemic, is one of the largest positive strand RNA viruses. Here we developed a simplified SPLASH assay and comprehensively mapped the in vivo RNA-RNA interactome of SARS-CoV-2 RNA during the viral life cycle. We observed canonical and alternative structures including 3-UTR and 5-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in cells and in virions. We provide direct evidence of interactions between Transcription Regulating Sequences (TRS-L and TRS-Bs), which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE, forming a "high-order pseudoknot" embedding FSE, which might help ribosome stalling at frameshift sites. More importantly, we found that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome cyclization is weakened and genome domains remain stable. Our data provides a structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, describes dynamics of RNA structures during life cycle of SARS-CoV-2, and will help to develop antiviral strategies.

SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China, and rapidly spread worldwide. Previous studies suggested cat could be a potential susceptible animal of SARS-CoV-2. Here, we investigated the infection of SARS-CoV-2 in cats by detecting specific serum antibodies. A cohort of serum samples were collected from cats in Wuhan, including 102 sampled after COVID-19 outbreak, and 39 prior to the outbreak. 15 of 102 (14.7%) cat sera collected after the outbreak were positive for the receptor binding domain (RBD) of SARS-CoV-2 by indirect enzyme linked immunosorbent assay (ELISA). Among the positive samples, 11 had SARS-CoV-2 neutralizing antibodies with a titer ranging from 1/20 to 1/1080. No serological cross-reactivity was detected between the SARS-CoV-2 and type I or II feline infectious peritonitis virus (FIPV). Our data demonstrates that SARS-CoV-2 has infected cat population in Wuhan during the outbreak.

Adaptive amino acid substitutions enable transmission of an H9N2 avian influenza virus in guinea pigs.

H9N2 is the most prevalent low pathogenic avian influenza virus (LPAIV) in domestic poultry in the world. Two distinct H9N2 poultry lineages, G1-like (A/quail/Hong Kong/G1/97) and Y280-like (A/Duck/Hong Kong/Y280/1997) viruses, are usually associated with binding affinity for both α 2,3 and α 2,6 sialic acid receptors (avian and human receptors), raising concern whether these viruses possess pandemic potential. To explore the impact of mouse adaptation on the transmissibility of a Y280-like virus A/Chicken/Hubei/214/2017(H9N2) (abbreviated as WT), we performed serial lung-to-lung passages of the WT virus in mice. The mouse-adapted variant (MA) exhibited enhanced pathogenicity and advantaged transmissibility after passaging in mice. Sequence analysis of the complete genomes of the MA virus revealed a total of 16 amino acid substitutions. These mutations distributed across 7 segments including PB2, PB1, PA, NP, HA, NA and NS1 genes. Furthermore, we generated a panel of recombinant or mutant H9N2 viruses using reverse genetics technology and confirmed that the PB2 gene governing the increased pathogenicity and transmissibility. The combinations of 340 K and 588 V in PB2 were important in determining the altered features. Our findings elucidate the specific mutations in PB2 contribute to the phenotype differences and emphasize the importance of monitoring the identified amino acid substitutions due to their potential threat to human health.

[Screening of proteins interacting with avian influenza virus nucleoprotein by yeast two-hybrid system in human brain cDNA library].

Avian influenza virus Nucleoprotein (NP) is important in viral transcription, replication and determining host specificity of influenza virus. Yeast two-hybrid technique was applied to screen for proteins interacting with virus nucleoprotein, so as to further elucidate the interaction between virus nucleoprotein and cellular proteins, as well as the interaction between virus and host. To explore new proteins interacted with NP protein, a human brain cDNA library was screened using yeast two-hybrid system with NP as the bait. DNA inserts of the positive AD/library plasmids were sequenced. By the BLAST analysis against the GenBank databases seven positive clones resulted in seven genes. Our results could help for the further study on the molecular mechanism of virus replication, transcription and protein-protein interaction. Further investigations were needed to characterize these interactions.

Identification of a surface protective antigen, HP0197 of Streptococcus suis serotype 2.

Streptococcus suis serotype 2 (SS2) is a porcine and human pathogen with adhesive and invasive properties. As traditional inactive vaccine has obvious shortcomings, to identify protective antigens would undoubtedly contribute to the development of novel vaccines. HP0197 has been identified as immunogenic protein in the previous study but its protective efficacy was not clear. In the present study, the purified recombinant HP0197 protein could elicit a significant humoral antibody response and could confer significant protection against challenge with lethal dose of SS2 in mice and pigs. In addition, the hyperimmune sera against HP0197 could efficiently kill the bacteria in the opsonized phagocytosis test and conferred significant protection against SS2 infection in the experiment of passive immunization. The present study suggests with strong evidence that the identified protective antigen would be a novel and an effective vaccine candidate for SS2.

The early diagnosis of lung carcinoma with normal plain CT scan / 复旦学报（医学版）

Objective To explore the diagnosis for early stage lung cancer with "normal" plain CT scan in order to draw the concern of physician to these patients. Methods We reviewed and analyzed 3 cases of central bronchogenic carcinoma with normal plain CT scan at first visit who were confirmed through fiber bronchoscope examination and PET/CT scan later. Then we compared the values of some diagnostic methods for early-stage central bronchogenic carcinoma. Results Three patients were all males with long smoking history. They came to hospital for cough and bloody sputum. All their plain CT scan showed "no abnormal findings", but their symptom continued. Later, the fiber bronchoscope examination and PET/CT scan strongly suggested that they were suffered from central bronchogenic carcinoma, and then the pathological findings and sputum cytology confirmed the diagnosis. Two patients received lobectomy, and the other one was suggested to accept radiotherapy because of his poor lung function. Conclusions The positive rate of plain CT scan for early-stage central bronchogenic carcinoma is relatively low. Thus, some of these patients lost the chance of surgery and combined therapy. So physicians should pay more attention to these patients with symptoms of persistent bloody sputum or obstructive pneumonia, even if the plain CT scan is negative at first visit. Using PET/CT and fiber bronchoscope examination, physicians can confirm the diagnosis of central bronchogenic carcinoma. So these two methods are important in the diagnosis for early-stage central bronchogenic carcinoma without any abnormal plain CT scan findings.

Prokaryotic expression of recombinant Streptococcus suis IgG binding protein and its binding activity with IgG / 生物工程学报

Streptococcus suis (S. suis) IgG-binding protein (SPG) was present in all S. suis strains examined. It showed binding activities with IgG from various host species. Little was known about the biological role of this protein, but it was commonly believed that it acted as virulence factor. In this study, the genes encoding SPG were amplified respectively from the total DNA of the S. suis serotype 1/2, 1, 2 and 9 with PCR and expressed in Escherichia coli BL21 by plasmid pET28a as vector. The recombinant proteins were first purified with affinity chromatography (Ni-NTA), and further purified by sephadexG-200 gel chromatography. The recombinant SPG proteins were identified to have binding activities with IgG of different host species, and for human and porcine IgG they showed better binding activities. But the SPG from different serotypes of S. suis showed no great differences in their binding activities with IgG from the same host species.

The rescue of H1N1 subtype swine influenza virus / 生物工程学报

The swine influenza virus (SIV) strain A/Swine/TianJin/01/2004(H1N1) (A/S/TJ/04) was rescued successfully by an eight-plasmid rescue system. The cDNAs of SIV 8 gene segments were synthesized by RT-PCR and cloned into the RNA polymerase I/II bidirection expression vector PHW2000 independently, resulting in 8 recombinant plasmids. The 8 recombinant plasmids were cotransfected into COS-1 cell, 30 h later TPCK-trypsin was added to 0.5 microg/mL. The COS-1 cell and supernatant were harvested 48 h after cotransfection and were inoculated into the allantoic cavity of 9-day-old specific-pathogen free (SPF) chicken eggs. The allantoic fluid of dead eggs was harvested and passaged 3 generations in SPF chicken eggs to get infective virus. The successful rescue of A/S/TJ/04 SIV was identified by hemagglutination assay, hemagglutination inhibition assay, sequence analysis and electron microscope observation. The successful rescue of SIV built a platform for the research of the relationship between genome structure and function of SIV, the mechanisms of trans-species transmission of influenza virus and for the generation of new SIV as vaccine.