Discovery of orally bioavailable SARS-CoV-2 papain-like protease inhibitor as a potential treatment for COVID-19 (preprint)

The RNA-dependent RNA polymerase (RdRp), 3C-like protease (3CLpro), and papain-like protease (PLpro) are pivotal components in the viral life cycle of SARS-CoV-2, presenting as promising therapeutic targets. Currently, all FDA-approved antiviral drugs against SARS-CoV-2 are RdRp or 3CLpro inhibitors. However, the mutations causing drug resistance have been observed in RdRp and 3CLpro from SARS-CoV-2, which makes it necessary to develop antivirals with novel mechanisms. Through the application of a structure-based drug design (SBDD) approach, we discovered a series of novel potent non-covalent PLpro inhibitors with remarkable in vitro potency and in vivo PK properties. The co-crystal structures of PLpro with leads revealed that the residues E164 and Q269 around the S2 site are critical for improving the inhibitor\'s potency. The lead compound GZNL-P36 not only inhibited SARS-CoV-2 and its variants at the cellular level with EC50 ranging from 58.2 nM to 306.2 nM, but also inhibited HCoV-NL63 and HCoV-229E with EC50 of 81.6 nM and 2.66 M, respectively. Oral administration of the compound resulted in significantly improved survival and notable reductions in lung viral loads and lesions in SARS-CoV-2 infection mouse model, consistent with RNA-seq data analysis. Our results indicate that PLpro inhibitor is a promising SARS-CoV-2 therapy.

Risks of digestive diseases in long COVID: Evidence from a large-scale cohort study (preprint)

Objectives: This study aims to evaluate the effect of coronavirus disease 2019 (COVID-19) on the long-term risk of digestive diseases in the general population. Design: Large-scale population-based cohort study based on a prospective cohort. Setting: UK Biobank cohort linked to multiple nationwide electronic health records databases. Participants: The cohort consisted of 112,311 individuals who survived the initial 30 days following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as well as two control groups: a contemporary group (n = 359,671) without any history of COVID-19, and a historical control group (n = 370,979) that predated the COVID-19 outbreak. Main outcome measures: Main outcomes were predefined digestive diseases. Hazard ratios and corresponding 95% confidence intervals (CI) were computed utilizing the Cox regression models after inverse probability weighting. Results: Compared with the contemporary control group, patients with previous COVID-19 infection had higher risks of digestive diseases, including functional gastrointestinal disorders (hazard ratios [HR] 1.95 (95% CI 1.62 to 2.35)); peptic ulcer disease (HR 1.27 (1.04 to 1.56)); gastroesophageal reflux disease (GERD) (HR 1.46 (1.34 to 1.58)); inflammatory bowel diseases (HR 1.40 (1.02 to 1.90)); gallbladder disease (HR 1.28 (1.13 to 1.46)); severe liver disease (HR 1.46 (1.12 to 1.90)); non-alcoholic liver disease (HR 1.33 (1.15 to 1.55)); and pancreatic disease (HR 1.43 (1.17 to 1.74)). The risks of GERD were stepwise increased with severity of the acute phase of COVID-19 infection. The results were consistent when using the historical cohort as the control group. Conclusions: Our study provides important insights into the association between COVID-19 and the long-term risk of digestive system disorders. COVID-19 patients are at a higher risk of developing gastrointestinal disorders, with stepwise increased risk with the severity and persisting even after one year follow-up.

Discovery and evaluation of active compounds from Xuanfei Baidu Formula against COVID-19 via SARS-Cov-2 Mpro (preprint)

Background The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2) is still a widespread concern. As one of the effective traditional Chinese medicine (TCM) formula, Xuanfei Baidu formula (XFBD) shows significant efficacy for treatment of COVID-19 patients. However, its antiviral compounds and mechanism are still unclear. Purpose: In this study, we explored the bioactive compounds of XFBD and its antiviral mechanism by integrating computational analysis and experimental testing. Methods Aiming at the SARS-CoV-2 main protease (Mpro), as a key target in virus replication, the fluorescence resonance energy transfer (FRET) assay was built to screen out satisfactory natural inhibitors from XFBD. The surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) were undertaken to verify the binding affinity of Mpro-ligand. Omicron BA.1.1 and BA.2 variants were used to evaluate the antiviral activity of the focused compounds in non-cytotoxicity concentrations. For introducing the molecular mechanism, computational modeling and NMR spectra were employed to predict the binding mode and binding site of Mpro-ligand. Results From a library of 83 natural compounds, acteoside, licochalcone B, licochalcone D, linoleic acid, and physcion showed the satisfactory inhibition effect on Mpro with IC50 from 1.93 to 42.96 µM, which were further verified by SPR. Showing the excellent binding affinity, acteoside was witnessed to gain valuable insights into the thermodynamic signatures by ITC and presented antiviral activity on Omicron BA.1.1 and BA.2.3 variants in vitro. The results revealed that acteoside inhibited Mpro via forming the hydrogen bond between 7-H of acteoside and Mpro. Conclusion Acteoside is regarded as a representative active natural compound in XFBD to inhibit replication of SARS-CoV-2, which provides the antiviral evidence and some insight into the identifications of SARS-CoV-2 Mpro natural inhibitors.

Predictive Value of Pulmonary Involvement Score and Clinical Parameters for Severe COVID-19: A Nomogram-Based Approach in Emergency Department (preprint)

Background This study aims to evaluate the prognostic value of a pulmonary involvement (PI) score in COVID-19 patients, both independently and in combination with clinical and laboratory parameters, following the adjustment of the dynamic zeroing policy in China.Methods A total of 288 confirmed COVID-19 pneumonia patients (mild/moderate group, 155; severe group, 133) from the Emergence Department, Beijing Chaoyang Hospital, were enrolled in this study and allocated to the training and validation cohort. The PI score of the initial chest CT was evaluated using a semi-quantitative scoring system, and clinical and laboratory parameters were collected. Radiomics and combination predictive models were developed using the least absolute shrinkage and selection operator (LASSO) logistic regression algorithm and multivariate logistic regression. The models' performance for predicting severe COVID-19 was assessed by receiver operating characteristics curve (ROC) analysis and calibration curve.Results Compared with the mild/moderate patients, the severe patients had higher levels of C-reactive protein (CRP), D-dimer, procalcitonin (PCT), and brain natriuretic peptide (BNP), but lower blood oxygen saturation and vaccination rate (P < 0.05). The severe group had a higher incidence of consolidation, multi-lobe involvement, interlobular septal thickening, air bronchogram sign, and pleural effusion compared to the mild/moderate group (P < 0.05). Moreover, the PI total score of severe patients was 16.4 ± 3.8, significantly higher than 8.5 ± 3.8 of milder patients (P < 0.001). The developed predictive nomogram, which includes four clinical characteristics and one CT feature, exhibited good performance in predicting severe COVID-19 with an area under the ROC (AUC) of 0.98 (95% CI, 0.97-1.00) in the training dataset, and 0.97 (95% CI, 0.94-1.00) in the validation dataset.Conclusions The combination predictive model, including CT score, clinical factors, and laboratory data, shows favorable predictive efficacy for severe COVID-19, which could potentially aid clinicians in triaging emergency patients.

Effectiveness of vero cell inactivated vaccine against severe acute respiratory infections (SARI) in Sibu, Malaysia: A retrospective test-negative design.

The effectiveness of the vero cell inactivated vaccine (CoronaVac®) against severe acute respiratory infection ( SARI) caused by SARS-CoV-2 in the real world was assessed. A matched test-negative case-control design was employed using the web-based national information system, as well as the hospitalization dataset in Sibu Hospital. Vaccine effectiveness was measured by conditional logistic regression with adjustment for gender, underlying comorbidity, smoking status, and education level. Between 15 March and 30 September 2021, 838 eligible SARI patients were identified from the hospitalization records. Vaccine effectiveness was 42.4% (95% confidence interval [CI]: -28.3 to 74.1) for partial vaccination (after receiving the first dose to 14 days after receiving the second dose), and 76.5% (95% CI: 45.6 to 89.8) for complete vaccination (at 15 days or more after receiving the second dose). This analysis indicated that two doses of CoronaVac® vaccine provided efficacious protection against SARI caused by SARS-CoV-2 in the short term. However, the duration of protection, and performance against new variants need to be studied continuously.

Improved Neutralization of Omicron BA.4/5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 with Bivalent BA.4/5 Vaccine (preprint)

The BNT162b2 bivalent BA.4/5 COVID-19 vaccine has been authorized to mitigate COVID-19 due to current Omicron and potentially future variants. New sublineages of SARS-CoV-2 Omicron continue to emerge and have acquired additional mutations, particularly in the spike protein, that may lead to improved viral fitness and immune evasion. The present study characterized neutralization activities against new Omicron sublineages BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 after a 4th dose (following three doses of BNT162b2) of either the original monovalent BNT162b2 or the bivalent BA.4/5 booster in individuals >55 years of age. For all participants, the 4th dose of monovalent BNT162b2 vaccine induced a 3.0, 2.9, 2.3, 2.1, 1.8, and 1.5 geometric mean neutralizing titer fold rise (GMFR) against USA/WA1-2020 (a strain isolated in January 2020), BA.4/5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1, respectively; the bivalent vaccine induced 5.8, 13.0, 11.1, 6.7, 8.7, and 4.8 GMFRs. For individuals without SARS-CoV-2 infection history, BNT162b2 monovalent induced 4.4, 3.0, 2.5, 2.0, 1.5, and 1.3 GMFRs, respectively; the bivalent vaccine induced 9.9, 26.4, 22.2, 8.4, 12.6, and 4.7 GMFRs. These data suggest the bivalent BA.4/5 vaccine is more immunogenic than the original BNT162b2 monovalent vaccine against circulating Omicron sublineages, including BQ.1.1 that is becoming prevalent globally.

Trophic state assessment of optically diverse lakes using Sentinel-3-derived trophic level index

An accurate estimation of trophic state of lakes with satellite remote sensing is a challenge due to the optical complexity and variability associated with inland waters. Match-up data from 393 sampling stations that has concurrent Sentinel-3 OLCI images were acquired across Wuhan lakes. Trophic Level Index (TLI) algorithms were developed within a global Optical Water Type (OWT) classification system. The performance of algorithms with limited training data gathered by using spectral similarity of highest Sowt was not improved compared with that on basis of no classification. In contrast, using spectral similarity of Sowt > 0.9 rather than the highest Sowt to group more training data with similar traits for each OWT can help build more robust algorithms, which performance is better than that on basis of no classification. Algorithm performance statistics of the test dataset for the stepwise multiple linear regression (SMLR) method were the following: Mean Absolute Error (MAE) = 5.56;Mean Absolute Percentage Error (MAPE) = 11.02 %;Root Mean Square Error (RMSE) = 7.24 and for the back propagation neural network on the basis of the Levenberg-Marquardt-Bayesian regularization algorithm (LMBR-BPNN) method MAE = 4.56;MAPE = 8.33 %;RMSE = 5.98. We detected 8 different OWTs (2,3,4,5,9,10,11,12) in Wuhan lakes and clear spatio-temporal patterns of the trophic state between 2018 and 2020.Our results revealed that the trophic state of Wuhan lakes did not decrease as expected during the COVID-19 lockdown period.

Exposure to BA.4/BA.5 Spike glycoprotein drives pan-Omicron neutralization in vaccine-experienced humans and mice (preprint)

The SARS-CoV-2 Omicron variant and its sublineages show pronounced viral escape from neutralizing antibodies elicited by vaccination or prior SARS-CoV-2 variant infection owing to over 30 amino acid alterations within the spike (S) glycoprotein. We and others have recently reported that breakthrough infection of vaccinated individuals with Omicron sublineages BA.1 and BA.2 are associated with distinct patterns of cross-neutralizing activity against SARS-CoV-2 variants of concern (VOCs). BA.2 breakthrough infection mediated overall stronger cross-neutralization of BA.2 and its descendants (BA.2.12.1, BA.4, and BA.5) compared to BA.1 breakthrough infection. Here we characterized the effect of Omicron BA.4/BA.5 S glycoprotein exposure on the magnitude and breadth of the neutralizing antibody response upon breakthrough infection in vaccinated individuals and in mice upon booster vaccination. We show that immune sera from triple mRNA-vaccinated individuals with subsequent Omicron BA.4/BA.5 breakthrough infection display broad and robust neutralizing activity against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/BA.5. Administration of a prototypic BA.4/BA.5-adapted mRNA booster vaccine to mice following SARS-CoV-2 wild-type strain-based primary immunization is associated with similarly broad neutralizing activity. Immunization of naive mice with a bivalent mRNA vaccine (wild-type + Omicron BA.4/BA.5) induces strong and broad neutralizing activity against Omicron VOCs and previous variants. These findings suggest that when administered as boosters, mono- and bivalent Omicron BA.4/BA.5-adapted vaccines may enhance neutralization breadth, and in a bivalent format may also have the potential to confer protection to individuals with no pre-existing immunity against SARS-CoV-2.

Associations of habitual fish oil use with risk of SARS-CoV-2 infection and COVID-19-related outcomes in UK: national population based cohort study (preprint)

Objectives To prospectively investigate the associations of habitual fish oil use with Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, hospital admission, or mortality with Corona Virus Disease-19 (COVID-19) in a large-scale cohort. Design Prospective population-based cohort study. Setting UK Biobank. Participants A total of 110 440 participants aged 37 -73 years who completed a questionnaire on supplement use, which included fish oil at baseline were enrolled between 2006 and 2010 and followed up until 2022. Main exposure All participants filled out questionnaires about the habitual use of supplements, including fish oil. Main outcome measures SARS-CoV-2 infection, COVID-19 hospital admission and COVID-19 mortality. Results At baseline, 29 424 (26.6%) of the 110 440 participants reported habitual use of fish oil supplements. The multivariable adjusted hazard ratios for habitual users of fish oil versus non-users were 0.95 (0.93 to 0.98) for SARS-CoV-2 infection among participants with follow-up time less than 12.1 years but no significant associations were observed for participants with follow-up time more than 12.1 years. For COVID-19-related outcomes, the hazard ratios were 0.79 (95% confidence interval 0.71 to 0.88) for COVID-19 hospital admission and 0.72 (0.60 to 0.87) for COVID-19 mortality. For COVID-19-related outcomes, the association seemed to be stronger among those with longstanding illness. The Cox proportional hazard analysis after propensity-score matching yielded consistent results. Conclusions Habitual fish oil supplement is associated with a lower risk of hospital admission and mortality with COVID-19, but not associated with SARS-CoV-2 infection in the population with more than 12.1 years of follow-up.

Associations of habitual glucosamine use with SARS-CoV-2 infection and hospital admission and death with COVID-19: Evidence from a large population based cohort study (preprint)

Objectives To assess the association of habitual glucosamine use with coronavirus 2 (SARS-CoV-2) infection, hospital admission, or mortality with Corona Virus Disease-19 (COVID-19) in a large population based cohort. Design Population based, prospective cohort study. Setting UK Biobank. Participants Participants with complete information on habitual glucosamine use and SARS-CoV-2 infection or COVID-19-related outcomes were included. These participants were registered from 2006 to 2010, followed up until 2022 and participated in SARS-CoV-2 tests between 2020 and 2022. Main outcome measures SARS-CoV-2 infection, COVID-19 hospital admission, and COVID-19 mortality. Results At baseline, 20,118 (15.9%) of the 126,518 participants reported as habitual glucosamine users. During the median follow-up 12.16 years, there were 53,682 cases of SARS-CoV-2 infection, 2,120 cases of COVID-19 hospital admission and 548 cases of COVID-19 mortality. The multivariate adjusted hazard ratios of habitual glucosamine users to non-users were 1.02 (95% confidence interval [CI] 0.99 to 1.05) for SARS-CoV-2 infection, 0.73 (95% CI 0.63 to 0.85) for COVID-19 hospital admission, and 0.74 (95% CI 0.56 to 0.98) for COVID-19 mortality. The Cox proportional hazard analysis after propensity-score matching yielded consistent results. Conclusions Habitual glucosamine use seems to be associated with a lower risk of hospital admission and mortality with COVID-19, but not the risk of SARS-CoV-2 infection.

Associations of proton pump inhibitors with susceptibility to pneumonia, influenza, and COVID-19: evidence from a large population based cohort study (preprint)

Objective Concerns have been raised about the widespread use of proton pump inhibitors (PPIs), and current findings linking the regular use of PPIs to respiratory infections remain inconsistent. Our study aims to evaluate whether PPI use increases the risk of pneumonia, influenza, and COVID-19. Method The presented study included 160,923 eligible participants from the UK Biobank (mean age 56.5 years, 53% women). Cox proportional hazards regression and propensity score-matching analyses were used to estimate the hazard ratios (HRs) and 95% confidence intervals (CIs). Effect modifications by stratifications, including indications and CYP2C19 phenotypes were tested. Results The regular use of PPIs was associated with increased risks of developing pneumonia (hazard ratio [HR] 1.42, 95% confidence interval [CI] 1.26-1.59) and influenza (HR 1.31, 95% CI 1.11-1.55). However, the risk of COVID-19 infection among regular PPI users was not significantly increased (HR 1.05, 95% CI 0.95-1.16). The burden was more notably observed in patients without indications of PPI use (HR 1.52, 95% CI 1.33-1.73 for pneumonia; HR 1.36, 95% CI 1.12-1.64 for influenza). The risk for pneumonia was higher among the CYP2C19 rapid and ultrarapid metabolizers (HR 1.45, 95% CI 1.22-1.73, P for interaction < 0.001). The propensity score-matching analyses yielded similar trends. Conclusions The regular use of PPIs is associated with increased susceptibility to pneumonia and influenza, but not COVID-19 infection. The risks are even higher among recipients without main indications. Our study highlights the appropriate use and de-prescribing of PPIs according to indications and CYP2C19 phenotypes for patients and clinical practitioners.

Efficacy of heterologous boosting against SARS-CoV-2 using a recombinant interferon-armed fusion protein vaccine (V-01): a randomized, double-blind and placebo-controlled phase III trial.

Waning of neutralizing titres along with decline of protection efficacy after the second dose of COVID-19 vaccines was observed, including China-made inactivated vaccines. Efficacy of a heterologous boosting using one dose of a recombinant SARS-CoV-2 fusion protein vaccine (V-01) in inactivated vaccine-primed population was studied, aimed to restore the immunity. A randomized, double-blind and placebo-controlled phase III trial was conducted in healthy people aged 18 years or older in Pakistan and Malaysia. Each eligible participant received one dose of the V-01 vaccine developed by Livzon Mabpharm Inc. or placebo within the 3-6 months after the two-dose primary regimen, and was monitored for safety and efficacy. The primary endpoint was protection against confirmed symptomatic SARS-CoV-2 infection. A total of 10,218 participants were randomly assigned to receive a vaccine or placebo. Virus-neutralizing antibodies were assessed in 419 participants. A dramatic increase (11.3-fold; 128.3-1452.8) of neutralizing titres was measured in the V-01 group at 14 days after the booster. Over two months of surveillance, vaccine efficacy was 47.8% (95%CI: 22.6-64.7) according to the intention-to-treat principle. The most common adverse events were transient, mild-to-moderate pain at the injection site, fever, headache, and fatigue. Serious adverse events occurred almost equally in V-01 (0.12%) and placebo (0.16%) groups. The heterologous boosting with the V-01 vaccine was safe and efficacious, which could elicit robust humoral immunity under the epidemic of the Omicron variant.Trial registration: ClinicalTrials.gov identifier: NCT05096832.

Neutralization of Omicron sublineages and Deltacron SARS-CoV-2 by 3 doses of BNT162b2 vaccine or BA.1 infection (preprint)

Distinct SARS-CoV-2 Omicron sublineages have evolved showing increased fitness and immune evasion than the original Omicron variant BA.1. Here we report the neutralization activity of sera from BNT162b2 vaccinated individuals or unimmunized Omicron BA.1-infected individuals against Omicron sublineages and Deltacron variant (XD). BNT162b2 post-dose 3 immune sera neutralized USA-WA1/2020, Omicron BA.1-, BA.2-, BA.2.12.1-, BA.3-, BA.4/5-, and XD-spike SARS-CoV-2s with geometric mean titers (GMTs) of 1335, 393, 298, 315, 216, 103, and 301, respectively; thus, BA.4/5 SARS-CoV-2 spike variant showed the highest propensity to evade vaccine neutralization compared to the original Omicron variants BA.1. BA.1-convalescent sera neutralized USA-WA1/2020, BA.1-, BA.2-, BA.2.12.1-, BA.3-, BA.4/5-, and Deltacron-spike SARS-CoV-2s with GMTs of 15, 430, 110, 109, 102, 25, and 284, respectively. The low neutralization titers of vaccinated sera or convalescent sera from BA.1 infected individuals against the emerging and rapidly spreading Omicron BA.4/5 variants provide important results for consideration in the selection of an updated vaccine in the current Omicron wave.

Impact of Covid-19 on economic recovery: empirical analysis from China and global economies

This research aims to utilize quarterly global VAR data from April 1, 2020, to September 30, 2021, to assess the influence of the economic recovery of China following the COVID-19 outbreak on global economies. China is one of the first big economies globally to show indications of recovery following the COVID-19 pandemic. The nation's economic growth has the biggest long-term influence on middle-income nations (0.17%) followed by low- and middle-income economies (0.16%) and high-income economies (0.16%) (0.15%). The chain reaction of China's economic growth is most visible in high-income nations (0.11–0.45%), followed by middle-income countries (0.08–0.33%) and low-income countries (0.02–0.05%). Our findings show that the post-COVID-19 economic rebound in China will mostly benefit middle-income nations, with low- and middle-income countries following closely after. After COVID-19, the influence of the economic recovery of China is most visible in the rise of energy consumption in high-income nations, followed by middle-income economies. It is also worth noting that the influence of China's economic expansion on low- and middle-income economies does not always imply a rise in energy consumption. Overall, China's economic recovery has a significantly stronger influence on other countries’ economic development than other countries’ energy consumption has on other economies’ growth.

Neutralization of Omicron BA.1, BA.2, and BA.3 SARS-CoV-2 by 3 doses of BNT162b2 vaccine (preprint)

The newly emerged Omicron SARS-CoV-2 has 3 distinct sublineages: BA.1, BA.2, and BA.3. BA.1 accounts for the initial surge and is being replaced by BA.2, whereas BA.3 is at a low prevalence at this time. Here we report the neutralization of BNT162b2-vaccinated sera (collected at 1 month after dose 3) against the three Omicron sublineages. To facilitate the neutralization testing, we engineered the complete BA.1, BA.2, or BA.3 spike into an mNeonGreen USA-WA1/2020 SRAS-CoV-2. All BNT162b2-vaccinated sera neutralized USA-WA1/2020, BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s with titers of >20; the neutralization geometric mean titers (GMTs) against the four viruses were 1211, 336, 300, and 190, respectively. Thus, the BA.1-, BA.2-, and BA.3-spike SARS-CoV-2s were 3.6-, 4.0-, and 6.4-fold less efficiently neutralized than the USA-WA1/2020, respectively. Our data have implications in vaccine strategy and understanding the biology of Omicron sublineages.

Neutralization of Omicron SARS-CoV-2 by 2 or 3 doses of BNT162b2 vaccine (preprint)

We report the antibody neutralization against Omicron SARS-CoV-2 after 2 and 3 doses of BNT162b2 mRNA vaccine. Vaccinated individuals were serially tested for their neutralization against wild-type SARS-CoV-2 (strain USA-WA1/2020) and an engineered USA-WA1/2020 bearing the Omicron spike glycoprotein. Plaque reduction neutralization results showed that at 2 or 4 weeks post-dose-2, the neutralization geometric mean titers (GMTs) were 511 and 20 against the wild-type and Omicron-spike viruses, respectively, suggesting that two doses of BNT162b2 were not sufficient to elicit robust neutralization against Omicron; at 1 month post-dose-3, the neutralization GMTs increased to 1342 and 336, respectively, indicating that three doses of vaccine increased the magnitude and breadth of neutralization against Omicron; at 4 months post-dose-3, the neutralization GMTs decreased to 820 and 171, respectively, suggesting similar neutralization decay kinetics for both variants. The data support a three-dose vaccine strategy and provide the first glimpse of the neutralization durability against Omicron.

Neutralization of SARS-CoV-2 Omicron pseudovirus by BNT162b2 vaccine-elicited human sera (preprint)

A new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage, B.1.1.529, was recently detected in Botswana and South Africa and is now circulating globally. Just two days after it was first reported to the World Health Organization (WHO), this strain was classified as a variant of concern (VOC) and named Omicron. Omicron has an unusually large number of mutations, including up to 39 amino acid modifications in the spike (S) protein, raising concerns that its recognition by neutralizing antibodies from convalescent and vaccinated individuals may be severely compromised. In this study, we tested pseudoviruses carrying the SARS-CoV-2 spike glycoproteins of either the Wuhan reference strain, the Beta, the Delta or the Omicron variants of concern with sera of 51 participants that received two doses or a third dose ([≥]6 months after dose 2) of the mRNA-based COVID-19 vaccine BNT162b2. Immune sera from individuals who received two doses of BNT162b2 had more than 22-fold reduced neutralizing titers against the Omicron as compared to the Wuhan pseudovirus. One month after a third dose of BNT162b2, the neutralization titer against Omicron was increased 23-fold compared to two doses and antibody titers were similar to those observed against the Wuhan pseudovirus after two doses of BNT162b2. These data suggest that a third dose of BNT162b2 may protect against Omicron-mediated COVID-19, but further analyses of longer-term antibody persistence and real-world effectiveness data are needed.

Six Month Safety and Efficacy of the BNT162b2 mRNA COVID-19 Vaccine (preprint)

Background: BNT162b2 is a lipid nanoparticle-formulated, nucleoside-modified RNA vaccine encoding a prefusion-stabilized, membrane-anchored SARS-CoV-2 full-length spike protein. BNT162b2 is highly efficacious against COVID-19 and is currently authorized for emergency use or conditional approval worldwide. At the time of authorization, data beyond 2 months post-vaccination were unavailable. Methods: In an ongoing, placebo-controlled, observer-blinded, multinational, pivotal efficacy study, 44,165 [≥]16-year-old participants and 2,264 12-15-year-old participants were randomized to receive 2 doses, 21 days apart, of 30 g BNT162b2 or placebo. Study endpoints reported here are vaccine efficacy (VE) against laboratory-confirmed COVID-19 and safety data, both up to 6 months post-vaccination. Results: BNT162b2 continued to be safe and well tolerated. Few participants had adverse events leading to study withdrawal. VE against COVID-19 was 91% (95% CI 89.0-93.2) through up to 6 months of follow-up, among evaluable participants and irrespective of previous SARS-CoV-2 infection. VE of 86%-100% was seen across countries and in populations with diverse characteristics of age, sex, race/ethnicity, and COVID-19 risk factors in participants without evidence of previous SARS-CoV-2 infection. VE against severe disease was 97% % (95% CI 80.3-99.9). In South Africa, where the SARS-CoV-2 variant of concern, B.1.351 (beta), was predominant, 100% (95% CI 53.5, 100.0) VE was observed. Conclusion: With up to 6 months of follow-up and despite a gradually declining trend in vaccine efficacy, BNT162b2 had a favorable safety profile and was highly efficacious in preventing COVID-19. (ClinicalTrials.gov number, NCT04368728)