Volume 04 · Issue 03 · 2022

Since its first discovery, the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evoked another wave of infection and caused global concern and panic. Moreover, although the data are still limited, Omicron showed highly concerning characteristics, including higher transmissibility, extensive immune escape and potentially altered host range. We interpreted these characteristics based on currently available data and outlined some urgent questions, calling for a more comprehensive investigation.

Omicron (B.1.1.529), the fifth variant of concern (VOC) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was firstly identified in November 2021 in South Africa. Omicron contains far more genome mutations than any other VOCs ever found, raising significant concerns about its increased transmissibility and immune evasion. Here, we report the importation of the Omicron variant into Beijing, China, in December 2021. Full-length genome sequences of five imported strains were obtained, with their genetic features characterized. Each strain contained 57 to 61 nucleotide substitutions, 39 deletions, and 9 insertions in the genome. Thirty to thirty-two amino acid changes were found in the spike proteins of the five strains. The phylogenetic tree constructed by the maximum likelihood method showed that all five imported genomes belonged to Omicron (BA.1) (alias of B.1.1.529.1), which is leading to the current surge of coronavirus disease 2019 (COVID-19) cases worldwide. The globally increased COVID-19 cases driven by the Omicron variant pose a significant challenge to disease prevention and control in China. Continuous viral genetic surveillance and increased testing among international travellers are required to contain this highly contagious variant.

Since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified during late 2019, the sustained spread of this pathogen within the human population has caused worldwide disruption with staggering infection rates and death tolls. Due to the accumulation of mutations in SARS-CoV-2, the virus has evolved into many variants, five of which have been listed as variants of concern VOCs by the World Health Organization (WHO). Multiple animal models of SARS-CoV-2 have been developed to evaluate vaccines and drugs and to assess the pathogenicity, transmissibility and antiviral measures of these VOCs. Here, we review the cutting-edge research based on mouse, hamster, ferret and non-human primate models for evaluating SARS-CoV-2 with a focus on the Omicron variant, and highlight the importance of updating vaccines in a timely manner in order to mitigate the negative effects of SARS-CoV-2 infections in the human population.

Due to the coronavirus disease 2019 (COVID-19) pandemic, the development of antiviral drugs has attracted increasing attention. Clinical antiviral drugs show weak solubility, low bioavailability, adverse side effects, or only limited targets. With the advancement of nanotechnology and material science, biosafety nanomaterials have been constructed for drug delivery systems of antiviral disease therapy, such as liposomes, polymers, gold nanoparticles, and graphene. These nanodrug systems can either deliver synthesized antiviral drugs siRNA/miRNA and small molecular compounds, deliver bioactive large molecular drug proteins and mRNA, or show antiviral activity by themselves. Nanodelivery systems could effectively enhance the efficiency of antiviral drugs by increasing drug loading and host cell uptake with a small size and high specific surface area. This review focused on the biosafety nanomaterials used for antiviral therapy and discussed the options for the design of antiviral drugs in the future.

The recently emerged Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has quickly spread around the world. Although many consensus mutations of the Omicron variant have been recognized, little is known about its genetic variation during its transmission in the population. Here, we comprehensively analyzed the genetic differentiation and diversity of the Omicron variant during its early outbreak. We found that Omicron achieved more structural variations, especially deletions, on the SARS-CoV-2 genome than the other four variants of concern (Alpha, Beta, Gamma, and Delta) in the same timescale. In addition, the Omicron variant acquired, except for 50 consensus mutations, seven great new non-synonymous nucleotide substitutions during its spread. Three of them are on the S protein, including S_A701V, S_L1081V, and S_R346K, which belong to the receptor-binding domain (RBD). The Omicron BA.1 branch could be divided into five divergent groups spreading across different countries and regions based on these seven novel mutations. Furthermore, we found that the Omicron variant possesses more mutations related to a faster transmission rate than the other SARS-CoV-2 variants by assessing the relationship between the genetic diversity and transmission rate. The findings indicated that more attention should be paid to the significant genetic differentiation and diversity of the Omicron variant for better disease prevention and control.

Like antibody evaluation, using an effective antigen-specific T-cell immunity assessment method in coronavirus disease 2019 (COVID-19) patients, survivors and vaccinees is crucial for understanding the immune persistence, prognosis assessment, and vaccine development for COVID-19. This study evaluated an empirically adjusted enzyme-linked immunospot assay for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T-cell immunity in 175 peripheral blood samples from COVID-19 convalescents and healthy individuals. Results of viral nucleic acid were used as the gold standard of infection confirmation. The SARS-CoV-2M peptide pool had higher sensitivity of 85% and specificity of 71% for the single peptide pool. For combined peptide pools, the parallel evaluation (at least one of the peptide pools is positive) of total peptide pools (S1&S2&M&N) had higher sensitivity (up to 93%), and the serial evaluation (all peptide pools are positive) of total peptide pools had higher specificity (up to 100%). The result of the serial evaluation was better than that of the parallel evaluation as a whole. The detection efficiency of M and N peptide pool serial evaluation appeared the highest, with a sensitivity of 80% and specificity of 93%. This T-cell immunity detection assay introduced in this report can achieve high operability and applicability. Therefore, it can be an effective SARS-CoV-2-specific cellular immune function evaluation method.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, generating new variants that pose a threat to global health; therefore, it is imperative to obtain safe and broad-spectrum antivirals against SARS-CoV-2 and its variants. To this end, we screened compounds for their ability to inhibit viral entry, which is a critical step in virus infection. Twenty compounds that have been previously reported to inhibit SARS-CoV-2 replication were tested by using pseudoviruses containing the spike protein from the original strain (SARS-CoV-2-WH01). The cytotoxicity of these compounds was determined. Furthermore, we identified six compounds with strong antagonistic activity against the WH01 pseudovirus, and low cytotoxicity was identified. These compounds were then evaluated for their efficacy against pseudoviruses expressing the spike protein from B.1.617.2 (Delta) and B.1.1.529 (Omicron), the two most prevalent circulating strains. These assays demonstrated that two phenothiazine compounds, trifluoperazine 2HCl and thioridazine HCl, inhibit the infection of Delta and Omicron pseudoviruses. Finally, we discovered that these two compounds were highly effective against authentic SARS-CoV-2 viruses, including the WH01, Delta, and Omicron strains. Our study identified potential broad-spectrum SARS-CoV-2 inhibitors and provided insights into the development of novel therapeutics.

Zika virus (ZIKV) may cause severe microcephaly in newborn babies and Guillain-Barré syndrome in some adults. In recent decades, its range has expanded in 86 countries. There are two ecologically and evolutionarily district cycles: urban cycle and sylvatic cycle. This work aimed to estimate the urban and sylvatic cycle areas of ZIKV throughout the world. The occurrence records of vectors, non-human primate hosts, and ZIKV were collected. We chose historical climate data, predicted vectors distribution, human population density, and elevation data as the variables to fit the maximum entropy model (MaxEnt). Current risk area and future prediction were performed with global climate models (GCMs) and shared socioeconomic pathways (SSPs). Predicting the ZIKV risk area would help tailor related control strategies. The results indicated that 16.6% of the world’s landmass (except Antarctica) is a risk area in the urban cycle. Approximately 6.22 billion people (78.69% of the global population) live in the risk area, with the vast majority in South Asia, tropical Africa, South America, North America, and countries around the Mediterranean Sea. Future climate change decreases the risk area of ZIKV. This study also suggested that the sylvatic cycle happened between the Tropic of Cancer and the Tropic of Capricorn. The overlap region of the urban and sylvatic cycles could be hotpots that ZIKV spill from the sylvatic to the urban cycle. It is indicated that long-term passenger screening, mosquito surveillance, and control are necessary.

The immune responses and the function of immune cells among asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection cases, especially in immuno-compromised individuals, remain largely unknown. Here we present a case of asymptomatic SARS-CoV-2 infection that lasted for at least 67 days. The patient has administrated Thymalfasin as 1.6 mg per dose every other day from Day 45 to 70, plus 200 mg per dose Arbidol antiviral therapy three doses per day from Day 48 to 57. Throughout the infection, no anti-SARS-CoV-2 specific IgM or IgG antibodies were detected. Instead, the patient showed either a low percentage or an absolute number of non-classical monocytes, dendritic cells (DCs), CD4+ T cells, and regulatory T cells (Tregs), which may account for the clinical feature and absence of antibody response. This case may shed new light on the outbreak management related to control/prevention, treatment, and vaccination of SARS-CoV-2 and other virus infections in immunocompromised individuals.