Precise Epitope Organization with Self‐adjuvant Framework Nucleic Acid for Efficient COVID‐19 Peptide Vaccine Construction

Peptide vaccines have advantages in easy fabrication and high safety, but their effectiveness is hampered by the poor immunogenicity of the epitopes themselves. Herein, we constructed a series of framework nucleic acids (FNAs) with regulated rigidity and size to precisely organize epitopes in order to reveal the influence of epitope spacing and carrier rigidity on the efficiency of peptide vaccines. We found that assembling epitopes on rigid tetrahedral FNAs (tFNAs) with the appropriate size could efficiently enhance their immunogenicity. Further, by integrating epitopes from SARS‐CoV‐2 on preferred tFNAs, we constructed a COVID‐19 peptide vaccine which could induce high titers of IgG against the receptor binding domain (RBD) of SARS‐CoV‐2 spike protein and increase the ratio of memory B and T cells in mice. Considering the good biocompatibility of tFNAs, our research provides a new idea for developing efficient peptide vaccines against viruses and possibly other diseases.

Precise Epitope Organization with Self-adjuvant Framework Nucleic Acid for Efficient COVID-19 Peptide Vaccine Construction.

Peptide vaccines have advantages in easy fabrication and high safety, but their effectiveness is hampered by the poor immunogenicity of the epitopes themselves. Herein, we constructed a series of framework nucleic acids (FNAs) with regulated rigidity and size to precisely organize epitopes in order to reveal the influence of epitope spacing and carrier rigidity on the efficiency of peptide vaccines. We found that assembling epitopes on rigid tetrahedral FNAs (tFNAs) with the appropriate size could efficiently enhance their immunogenicity. Further, by integrating epitopes from SARS-CoV-2 on preferred tFNAs, we constructed a COVID-19 peptide vaccine which could induce high titers of IgG against the receptor binding domain (RBD) of SARS-CoV-2 spike protein and increase the ratio of memory B and T cells in mice. Considering the good biocompatibility of tFNAs, our research provides a new idea for developing efficient peptide vaccines against viruses and possibly other diseases.

Advancing pathogen detection for airborne diseases

Airborne diseases including SARS, bird flu, and the ongoing Coronavirus Disease 2019 (COVID-19) have stimulated the demand for developing novel bioassay methods competent for early-stage diagnosis and large-scale screening. Here, we briefly summarize the state-of-the-art methods for the detection of infectious pathogens and discuss key challenges. We highlight the trend for next-generation technologies benefiting from multidisciplinary advances in microfabrication, nanotechnology and synthetic biology, which allow sensitive, rapid yet inexpensive pathogen assays with portable intelligent device.

Correction: A smartphone-based three-in-one biosensor for co-detection of SARS-CoV-2 viral RNA, antigen and antibody.

Correction for 'A smartphone-based three-in-one biosensor for co-detection of SARS-CoV-2 viral RNA, antigen and antibody' by Yanzhi Dou et al., Chem. Commun., 2022, DOI: https://doi.org/10.1039/d2cc01297a.

A smartphone-based three-in-one biosensor for co-detection of SARS-CoV-2 viral RNA, antigen and antibody.

Rapid and comprehensive diagnostic methods are necessary for early identification and monitoring of SARS-CoV-2. Here, we have developed a universal and portable three-in-one biosensor linked to a smartphone for co-detection of SARS-CoV-2 viral RNA, antigen, and antibody. In combination with a smartphone, the online monitoring of SARS-CoV-2 virus-infected patients from infection to immunization could be intelligently achieved.

Rapid and ultrasensitive electromechanical detection of ions, biomolecules and SARS-CoV-2 RNA in unamplified samples.

The detection of samples at ultralow concentrations (one to ten copies in 100 µl) in biofluids is hampered by the orders-of-magnitude higher amounts of 'background' biomolecules. Here we report a molecular system, immobilized on a liquid-gated graphene field-effect transistor and consisting of an aptamer probe bound to a flexible single-stranded DNA cantilever linked to a self-assembled stiff tetrahedral double-stranded DNA structure, for the rapid and ultrasensitive electromechanical detection (down to one to two copies in 100 µl) of unamplified nucleic acids in biofluids, and also of ions, small molecules and proteins, as we show for Hg2+, adenosine 5'-triphosphate and thrombin. We implemented an electromechanical biosensor for the detection of SARS-CoV-2 into an integrated and portable prototype device, and show that it detected SARS-CoV-2 RNA in less than four minutes in all nasopharyngeal samples from 33 patients with COVID-19 (with cycle threshold values of 24.9-41.3) and in none of the 54 COVID-19-negative controls, without the need for RNA extraction or nucleic acid amplification.

Sequential Therapy of Acute Kidney Injury with a DNA Nanodevice.

The high demand for acute kidney injury (AKI) therapy calls the development of multifunctional nanomedicine for renal management with programmable pharmacokinetics. Here, we developed a renal-accumulating DNA nanodevice with exclusive kidney retention for longitudinal protection of AKI in different stages in a renal ischemia-reperfusion (I/R) model. Due to the prolonged kidney retention time (>12 h), the ROS-sensitive nucleic acids of the nanodevice could effectively alleviate oxidative stress by scavenging ROS in stage I, and then the anticomplement component 5a (aC5a) aptamer loaded nanodevice could sequentially suppress the inflammatory responses by blocking C5a in stage II, which is directly related to the cytokine storm. This sequential therapy provides durable and pathogenic treatment of kidney dysfunction based on successive pathophysiological events induced by I/R, which holds great promise for renal management and the suppression of the cytokine storm in more broad settings including COVID-19.

COVID-19: A Call for Physical Scientists and Engineers.

The COVID-19 pandemic is one of those global challenges that transcends territorial, political, ideological, religious, cultural, and certainly academic boundaries. Public health and healthcare workers are at the frontline, working to contain and to mitigate the spread of this disease. Although intervening biological and immunological responses against viral infection may seem far from the physical sciences and engineering that typically work with inanimate objects, there actually is much that can-and should-be done to help in this global crisis. In this Perspective, we convert the basics of infectious respiratory diseases and viruses into physical sciences and engineering intuitions, and through this exercise, we present examples of questions, hypotheses, and research needs identified based on clinicians' experiences. We hope researchers in the physical sciences and engineering will proactively study these challenges, develop new hypotheses, define new research areas, and work with biological researchers, healthcare, and public health professionals to create user-centered solutions and to inform the general public, so that we can better address the many challenges associated with the transmission and spread of infectious respiratory diseases.

SARS-CoV-2 RNA reference materials

Coronavirus disease (COVID-19) is an acute infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Reverse transcription real-time fluorescent quantitative polymerase chain reaction (RT-qPCR) was the firstly authorized method for the detection of SARS-CoV-2 RNA. As this method is sensitive, specific, it has been widely recognized as the golden standard for the diagnosis of COVID-19. Unfortunately, several false-negative cases have been reported after the outbreak of COVID-19, probably due to the quality of the kits or the improper operation of RT-qPCR. Nucleic acid reference materials (RM) are the key element for the metrology traceability and quality control of SARS-CoV-2 RNA detection, but the development of RNA RM remains a challenge in the biology metrology field. Two main problems are the low stability of the RNA sample and the lack of proven absolute quantification methods. To establish the measurement traceability for SARS-CoV-2 RNA detection, a novel RNA reference material (RM) was developed. The RM is a mixed solution of 3 in vitro transcribed RNA molecules which cover different key target sequences of SARS-CoV-2 gene: The full-length of nucleoprotein (N) gene (28274-29533, GenBank: MT027064.1), the full-length of envelope protein (E) gene (26245-26472, GenBank: MT027064.1), and partial sequence of open reading frame 1ab (ORF1ab) (13321-15540, GenBank: MT027064.1). The purity of the transcribed RNA molecules was verified by a biological analyzer. The results showed that the molecular length of all the RNA molecules were consistent with our design. The clear peaks of our RNA RMs strongly demonstrated good purity. For absolute quantification of RNA RMs, we studied digital PCR (dPCR) for RNA samples. Digital PCR evenly partitioned the sample and PCR reaction solution to a very large number of units, on a microporous chip or in the liquid droplets, etc. After a PCR amplification reaction, the fluorescence signal was detected for each unit individually, with a binary readout of "0" or "1" for negative and positive results respectively. Through the statistics of positive results based on the Poisson distribution, the copy number of RNA sample was accurately determined without standard curves needed. Digital PCR has significantly higher reliability and accuracy. Mainly based on the PCR primers and probes for SARS-CoV-2 detection suggested by the Chinese CDC and WHO, we optimized the key factors of dPCR towards improved amplification efficiency. Through digital PCR measurements by 4 laboratories, the certified values of concentration (copies/mu L) were assigned for the N gene, E gene, and ORF1ab gene in the mixed RM. Single-stranded RNA is unstable and easy to be degraded by RNase in the environment, thus the optimization of RNA protectants is very important for the stability of RNA RMs. During the study of the stability, we found that a proper protector (1 mmol/L DTT and 0.5 U/L Rnase Inhibitor) can effectively increase the valid storage life of our RNA RM. Based on the latest data, the concentration of our RNA RMs was stable for at least 30 d under -80 degrees C storage and 13 d under -4 degrees C storage. In order to verify the applicability of our RNA RM in the actual virus detection process, we analyzed our RMs using 9 SARS-CoV-2 nucleic acid detection kits. These virus RNA detection kits were from different manufacturers with various detection principles, that are being applied in laboratories for virus detection. Finally, our RNA RMs showed high generalizability among 9 kits. The development of RNA RM provides the metrological basis for the quality control of SARS-CoV-2 detection kits.