De novo design of ACE2 protein decoys to neutralize SARS-CoV-2

There is an urgent need for the ability to rapidly develop effective countermeasures for emerging biological threats, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the ongoing coronavirus disease 2019 (COVID-19) pandemic. We have developed a generalized computational design strategy to rapidly engineer de novo proteins that precisely recapitulate the protein surface targeted by biological agents, like viruses, to gain entry into cells. The designed proteins act as decoys that block cellular entry and aim to be resilient to viral mutational escape. Using our novel platform, in less than ten weeks, we engineered, validated, and optimized de novo protein decoys of human angiotensin-converting enzyme 2 (hACE2), the membrane-associated protein that SARS-CoV-2 exploits to infect cells. Our optimized designs are hyperstable de novo proteins ([~]18-37 kDa), have high affinity for the SARS-CoV-2 receptor binding domain (RBD) and can potently inhibit the virus infection and replication in vitro. Future refinements to our strategy can enable the rapid development of other therapeutic de novo protein decoys, not limited to neutralizing viruses, but to combat any agent that explicitly interacts with cell surface proteins to cause disease.

Transmission routes of Covid-19 virus in the Diamond Princess Cruise ship

BackgroundAn outbreak of COVID-19 occurred on the Diamond Princess cruise ship in January and February 2020. We analysed information about cases to infer transmission dynamics and potential modes of transmission. MethodsWe collected the daily number of 197 symptomatic cases, and that of the 146 passenger cases in two categories, i.e. those who stayed and did not stay in the same stateroom. We retrieved the quarantine details and the ships 14-day itinerary. We searched the websites of national/local health authority along the cruise routes and local news using Google for locally confirmed cases associated with the ship. We obtained the design of air conditioning and sewage treatment of the ship from literature. We back-calculated the dates of infection from the epidemic curve and compared with the start of on-board quarantine. ResultsMajor infections started on Jan 28 and completed by Feb 6 for passengers except those who stayed in the same stateroom with infected individual(s). No other confirmed cases were identified among the disembarked people in Hong Kong except an 80 years old passenger. No confirmed cases were reported in three other stopovers between Jan 27-31 associated with disembarked passengers or visitors from the ship, however two Okinawa taxi drivers became confirmed cases in association with driving the ship passengers. Infection among passengers after Feb 6 was limited to those who stayed in the same stateroom with an infected passenger. Infections in crew members peaked on Feb 7, suggesting significant transmission among crew members after quarantine on Feb 5. ConclusionsWe infer that the ship central air conditioning system did not play a role, i.e. the long-range airborne route was absent in the outbreak. Most transmission appears to have occurred through close contact and fomites. Significance StatementTransmission by the long-range airborne route for SARS-CoV-2 in the 2020 Diamond Princess Covid-19 outbreak has been debated with significant implication for intervention. We found that the transmission by close contact and fomite explains the outbreak, and the central air-conditioning system did not play a role, demonstrating the importance of social distancing, good hygiene and maintaining good building ventilation for intervention.

Toilets dominate environmental detection of SARS-CoV-2 virus in a hospital

BackgroundRespiratory and faecal aerosols play a suspected role in transmitting the SARS-CoV-2 virus. We performed extensive environmental sampling in a dedicated hospital building for Covid-19 patients in both toilet and non-toilet environments, and analysed the associated environmental factors. MethodsWe collected data of the Covid-19 patients. 107 surface samples, 46 air samples, two exhaled condensate samples, and two expired air samples were collected were collected within and beyond the four three-bed isolation rooms. We reviewed the environmental design of the building and the cleaning routines. We conducted field measurement of airflow and CO2 concentrations. FindingsThe 107 surface samples comprised 37 from toilets, 34 from other surfaces in isolation rooms (ventilated at 30-60 L/s), and 36 from other surfaces outside isolation rooms in the hospital. Four of these samples were positive, namely two ward door-handles, one bathroom toilet-seat cover and one bathroom door-handle; and three were weakly positive, namely one bathroom toilet seat, one bathroom washbasin tap lever and one bathroom ceiling-exhaust louvre. One of the 46 air samples was weakly positive, and this was a corridor air sample. The two exhaled condensate samples and the two expired air samples were negative. InterpretationThe faecal-derived aerosols in patients toilets contained most of the detected SARS-CoV-2 virus in the hospital, highlighting the importance of surface and hand hygiene for intervention. FundingThe work were partially supported by the National Natural Science Foundation of China (no 41977370), the Research Grants Council of Hong Kongs (no 17202719) (no C7025-16G), and Scientific Research Fund of Jiangsu Provincial Department of Health (no S21017002).

Role of 1'-Ribose Cyano Substitution for Remdesivir to Effectively Inhibit both Nucleotide Addition and Proofreading in SARS-CoV-2 Viral RNA Replication

COVID-19 has recently caused a global health crisis and an effective interventional therapy is urgently needed. SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is a promising but challenging drug target due to its intrinsic proofreading exoribonuclease (ExoN). Remdesivir targeting SARS-CoV-2 RdRp exerts high drug efficacy in vitro and in vivo. However, its underlying inhibitory mechanisms remain elusive. Here, we performed all-atom molecular dynamics simulations with an accumulated simulation time of 24 microseconds to elucidate the molecular mechanisms underlying the inhibitory effects of Remdesivir. We found that Remdesivirs 1-cyano group of possesses the dual role of inhibiting nucleotide addition and proofreading. The presence of its polar 1-cyano group at an upstream site in RdRp causes instability and hampers RdRp translocation. This leads to a delayed chain termination of RNA extension, which may also subsequently reduce the likelihood for Remdesivir to be cleaved by ExoN acting on the 3-terminal nucleotide. In addition, our simulations suggest that Remdesivirs 1-cyano group can also disrupt the cleavage active site of ExoN via steric interactions, leading to a further reduced cleavage efficiency. Our work provides plausible molecular mechanisms on how Remdesivir inhibits viral RNA replication and may guide rational design for new treatments of COVID-19 targeting viral replication.

Short-range airborne route dominates exposure of respiratory infection during close contact

A susceptible person experiences the highest exposure risk of respiratory infection when he or she is in close proximity with an infected person. The large droplet route has been commonly believed to be dominant for most respiratory infections since the early 20th century, and the associated droplet precaution is widely known and practiced in hospitals and in the community. The mechanism of exposure to droplets expired at close contact, however, remains surprisingly unexplored. In this study, the exposure to exhaled droplets during close contact (< 2 m) via both the short-range airborne and large droplet sub-routes is studied using a simple mathematical model of expired flows and droplet dispersion/deposition/inhalation, which enables the calculation of exposure due to both deposition and inhalation. The short-range airborne route is found to dominate at most distances studied during both talking and coughing. The large droplet route only dominates when the droplets are larger than 100 m and when the subjects are within 0.2 m while talking or 0.5 m while coughing. The smaller the exhaled droplets, the more important the short-range airborne route. The large droplet route contributes less than 10% of exposure when the droplets are smaller than 50 m and when the subjects are more than 0.3 m apart, even while coughing. Practical implicationsOur simple but novel analysis shows that conventional surgical masks are not effective if most infectious viruses are contained in fine droplets, and non-conventional intervention methods such as personalised ventilation should be considered as infection prevention strategies given the possible dominance of the short-range airborne route, although further clinical evidence is needed. NomenclatureO_ST_ABSSubscriptC_ST_ABSi Droplets of different diameter groups (i = 1, 2, ..., N) LD Large droplet route SR Short-range airborne route SymbolsA0 Area of source mouth [m2] AE Aspiration efficiency [-] Ar0 Archimedes number [-] bg Gaussian half width [m] bt Top-hat half width [m] CD Drag coefficient [-] CI Specific heat of liquid [J*kg-1*K-1] Cs Specific heat of solid [J*kg-1*K-1] CT Correction factor for diffusion coefficient due to temperature dependence [-] dd Droplet diameter [m] dd0 Droplet initial diameter [m] de1 Major axis of eye ellipse [m] de2 Minor axis of eye ellipse [m] dh Characteristic diameter of human head [m] dm Mouth diameter [m] dn Nostril diameter [m] D{infty} Binary diffusion coefficient far from droplet [m2*s-1] DE Deposition efficiency [-] eLD Exposure due to large droplet route [L] eSR Exposure due to short-range airborne route [L] g Gravitational acceleration [m*s-2] Iv Mass current [kg*s-1] IF Inhalation fraction [-] Kc Constant (=0.3) [-] Kg Thermal conductivity of air [W*m-1*K-1] LS Exposure ratio between large droplet and short-range airborne [-] Lv Latent heat of vaporization [J*kg-1] md Droplet mass [kg] mI Mass of liquid in a droplet [kg] ms Mass of solid in a droplet [kg] M0 Jet initial momentum [m4*s-2] MW Molecular weight of H2O [kg*mol-1] MF Membrane fraction [-] n Number of droplets [n] n0 Number of droplets expelled immediately at mouth [n] Nin Number of droplets entering the inhalation zone [n] Nm Number of droplets potentially deposited on mucous membranes [n] Nt Total number of released droplets [n] Nu Nusselt number [-] p Total pressure [Pa] pv{infty} Vapour pressure distant from droplet surface [Pa] pvs Vapour pressure at droplet surface [Pa] Qjet Jet flow rate [m3*s-1] r Radial distance away from jet centreline [m] rd Droplet radius [m] R Radius of jet potential core [m] Rg Universal gas constant [J*K-1*mol-1] s Jet centreline trajectory length [m] Sin Width of region on sampler enclosed by limiting stream surface [m] Sh Sherwood number [-] Stc Stokes number in convergent part of air stream [-] Sth Stokes number for head [-] Stm Stokes number for mouth [-] t Time [s] T0 Initial temperature of jet [K] T{infty} Ambient temperature [K] Td Droplet temperature [K] u0 Initial velocity at mouth outlet [m*s-1] ud Droplet velocity [m*s-1] ug Gaussian velocity [m*s-1] ugas Gas velocity [m*s-1] ugc Gaussian centreline velocity [m*s-1] uin Inhalation velocity [m*s-1] ut Top-hat velocity [m*s-1] vp Individual droplet volume considering evaporation [m3] x Horizontal distance between source and target [m] z Jet vertical centreline position [m] {rho}0 Jet initial density [kg*m-3] {rho}{infty}Ambient air density [kg*m-3] {rho}d Droplet density [kg*m-3] {rho}g Gas density [kg*m-3] {Delta}{rho}Density difference between jet and ambient air [kg*m-3] g Gas dynamic viscosity [Pa*s] {varphi}Sampling ratio in axisymmetric flow system [-] c Impaction efficiency in convergent part of air stream [-]

Stability of SARS-CoV-2 in different environmental conditions

Stability of SARS-CoV-2 in different environmental conditions.

Conservation of T cell epitopes between seasonal inlfuenza viruses and the novel inlfuenza A H7N9 virus / 中国病毒学·英文版

A novel avian influenza A (H7N9) virus recently emerged in the Yangtze River delta and caused diseases, often severe, in over 130 people. This H7N9 virus appeared to infect humans with greater ease than previous avian inlfuenza virus subtypes such as H5N1 and H9N2. While there are other potential explanations for this large number of human infections with an avian influenza virus, we investigated whether a lack of conserved T-cell epitopes between endemic H1N1 and H3N2 inlfuenza viruses and the novel H7N9 virus contributes to this observation. Here we demonstrate that a number of T cell epitopes are conserved between endemic H1N1 and H3N2 viruses and H7N9 virus. Most of these conserved epitopes are from viral internal proteins. The extent of conservation between endemic human seasonal inlfuenza and avian inlfuenza H7N9 was comparable to that with the highly pathogenic avian inlfuenza H5N1. Thus, the ease of inter-species transmission of H7N9 viruses (compared with avian H5N1 viruses) cannot be attributed to the lack of conservation of such T cell epitopes. On the contrary, our ifndings predict signiifcant T-cell based cross-reactions in the human population to the novel H7N9 virus. Our findings also have implications for H7N9 virus vaccine design.