Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis

Mutational dynamics of SARS-CoV-2: Impact on future COVID-19 vaccine strategies

The rapid emergence of multiple strains of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has sparked profound concerns regarding the ongoing evolution of the virus and its potential impact on global health. Classified by the World Health Organization (WHO) as variants of concern (VOC), these strains exhibit heightened transmissibility and pathogenicity, posing significant challenges to existing vaccine strategies. Despite widespread vaccination efforts, the continual evolution of SARS-CoV-2 variants presents a formidable obstacle to achieving herd immunity. Of particular concern is the coronavirus spike (S) protein, a pivotal viral surface protein crucial for host cell entry and infectivity. Mutations within the S protein have been shown to enhance transmissibility and confer resistance to antibody-mediated neutralization, undermining the efficacy of traditional vaccine platforms. Moreover, the S protein undergoes rapid molecular evolution under selective immune pressure, leading to the emergence of diverse variants with distinct mutation profiles. This review underscores the urgent need for vigilance and adaptation in vaccine development efforts to combat the evolving landscape of SARS-CoV-2 mutations and ensure the long-term effectiveness of global immunization campaigns.

Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics

We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 spike (S) protein. With this approach, we first identified candidate adaptive polymorphisms (CAPs) of the SARS-CoV-2 S protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.

SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies

Since the SARS-CoV-2 Omicron virus has gained dominance worldwide, its continual evolution with unpredictable mutations and patterns has revoked all authorized immunotherapeutics. Rapid viral evolution has also necessitated several rounds of vaccine updates in order to provide adequate immune protection. It remains imperative to understand how Omicron evolves into different subvariants and causes immune escape as this could help reevaluate the current intervention strategies mostly implemented in the clinics as emergency measures to counter the pandemic and, importantly, develop new solutions. Here, we provide a review focusing on the major events of Omicron viral evolution, including the features of spike mutation that lead to immune evasion against monoclonal antibody (mAb) therapy and vaccination, and suggest alternative durable options such as the ACE2-based experimental therapies superior to mAbs to address this unprecedented evolution of Omicron virus. In addition, this type of unique ACE2-based virus-trapping molecules can counter all zoonotic SARS coronaviruses, either from unknown animal hosts or from established wild-life reservoirs of SARS-CoV-2, and even seasonal alpha coronavirus NL63 that depends on human ACE2 for infection.

Computational analysis of affinity dynamics between the variants of SARS-CoV-2 spike protein (RBD) and human ACE-2 receptor

The novel coronavirus SARS-CoV-2 resulted in a significant worldwide health emergency known as the COVID-19 pandemic. This crisis has been marked by the widespread of various variants, with certain ones causing notable apprehension. In this study, we harnessed computational techniques to scrutinize these Variants of Concern (VOCs), including various Omicron subvariants. Our approach involved the use of protein structure prediction algorithms and molecular docking techniques, we have investigated the effects of mutations within the Receptor Binding Domain (RBD) of SARS-CoV-2 and how these mutations influence its interactions with the human angiotensin-converting enzyme 2 (hACE-2) receptor. Further we have predicted the structural alterations in the RBD of naturally occurring SARS-CoV-2 variants using the tr-Rosetta algorithm. Subsequent docking and binding analysis employing HADDOCK and PRODIGY illuminated crucial interactions occurring at the Receptor-Binding Motif (RBM). Our findings revealed a hierarchy of increased binding affinity between the human ACE2 receptor and the various RBDs, in the order of wild type (Wuhan-strain) < Beta < Alpha < Gamma < Omicron-B.1.1.529 < Delta < Omicron-BA.2.12.1 < Omicron-BA.5.2.1 < Omicron-BA.1.1. Notably, Omicron-BA.1.1 demonstrated the highest binding affinity of -17.4 kcal mol-1 to the hACE2 receptor when compared to all the mutant complexes. Additionally, our examination indicated that mutations occurring in active residues of the Receptor Binding Domain (RBD) consistently improved the binding affinity and intermolecular interactions in all mutant complexes. Analysis of the differences among variants has laid a foundation for the structure-based drug design targeting the RBD region of SARS-CoV-2.

SARS-CoV-2 Pandemic: A Comparison Between the Epidemiological Situation in Greece and Romania

Introduction Since the onset of the SARS-CoV-2 pandemic, there seems to be scarce data targeting the comparison of epidemiological data among different countries. In an attempt to reveal and characterize the epidemiological profile in the Balkan peninsula, a cross-sectional study has been conducted, aiming to retrospectively collect all the existing information regarding the SARS-CoV-2 pandemic over a period of three years, starting from March 2020 until March 2023. The comparative analysis of the epidemiological features and the main indicators between Romania and Greece can generate a good overview of the factors that can influence public health and create an adequate system of measures to limit the COVID-19 pandemic in the area. A retrospective comparative study aiming to detect and associate the main indicators determining the evolution of the SARS-CoV-2 pandemic data with the control measures adopted in Romania and Greece was performed. Methods Publicly available data were obtained from official sources such as the World Health Organization, the European Centre for Disease Control, the Romanian and Greek Ministries of Health, and the Romanian National Centre for Surveillance and Control of Communicable Diseases. The reported number of cases, in total and in conjunction with the age distribution, total number of deaths, and vaccination coverage, from the onset of the pandemic in March 2020 until March 2023, were collected. All officially reported cases of COVID-19 were included in this analysis. Reports with missing or incomplete values regarding the timeframe, age distribution, and vaccination status were excluded. Results During the timeframe of the study, from March 2020 until March 2023, Greece reported a higher number of confirmed SARS-CoV-2 cases as compared to Romania (5,910,103 cases and 3,352,356 cases, respectively). Still, in terms of the overall death toll, Romania recorded a higher mortality rate than Greece during the pandemic (67.773 deaths vs. 36.372 deaths). Concerning both cumulative incidence rates and the 14-day case notification rate per 100.000 inhabitants, it is evident that Romania exhibited greater numbers throughout the course of the pandemic. Although it is not clearly stated, the compulsory vaccination of elderly people that was set as a high priority in Greece may have contributed to the above results. In terms of the 14-day death notification rate per 100.000 inhabitants in 2020 and 2021, Romania showed a higher rate than Greece, while Greece reported a greater rate in 2022 and up until March 2023. Between 2020 and 2023, Greece presented both a higher number of vaccinated individuals and a higher vaccination coverage with two doses (7,034,695 individuals, 70% of the general population), as compared to Romania (6,467,804 individuals, 33.68% of the general population, p<0.0001). Conclusions Despite the similar restrictions and preventive actions adopted by Romania and Greece, some of the epidemiological data between the two countries tends to differ. It must not be ignored that every nation should be considered a unique entity with distinct features, including individuals, customs, and policies, rather than being categorized with other countries based on geographic proximity or regionalization.

Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics

We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 Spike (S) protein. With this approach, we first identified Candidate Adaptive Polymorphisms (CAPs) of the SARS-CoV-2 Spike protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) primer design based on Indonesia SARS-CoV-2 RNA sequence

BACKGROUND

The COVID-19 pandemic has highlighted the importance of tracking cases by using various methods such as the Reverse transcription loop-mediated isothermal amplification (RT-LAMP) which is a fast, simple, inexpensive, and accurate mass tracker. However, there have been no reports about the development of RT-LAMP primer designs that use genome sequences of viruses from Indonesia. Therefore, this study aimed to design an RT-LAMP primer using SARS-CoV-2 genome sequences from Indonesia and several other countries representing five continents in the world, as well as genomes from five Variants of Concern (VOC).

RESULT

The results showed that the consensus sequence of 70 SARS-CoV-2 virus sequences was obtained with a length of 29,982 bases. The phylogenetic test confirmed that the consensus sequence had a close kinship with the SARS-CoV-2 Wuhan Isolate. Furthermore, the SimPlot analysis showed that there was a high genetic diversity of sequences from the Coronaviridae tribal virus at base sequences of 1,500-5,000, 6,500-7,500, and 23,300-25,500. A total of 139 sets of primers were obtained from the primer design with 4 sets namely T1_6, T1_9, T4_7, and T4_52 having the best characteristics. Based on the secondary structure analysis test on 4 sets of primers, T1_6 and T1_9 were predicted not to form secondary structures at RT-LAMP operational temperatures. The primer set T1_9 showed better specificity in BLAST NCBI and eLAMP BLAST tests.

CONCLUSION

This study obtained a primer set of T1_9 with base sequence F3: CACTGAGACTCATTGATGCTATG, B3: CCAACCGTCTCTAAGAAACTCT, F2: GTTCACATCTGATTTGGCTACT, F1c: GAAGTCAACTGAACAACACCACCT, B2: CCTTCCTTAAACTTCTCTTCAAGC, B1c: GTGGCTAACTAACATCTTTGGCACT, LB: TGAAAACAAACCCGCCGTCCTTG, which meets the ideal parameters and has the best specificity. Therefore, it is recommended for use in further tests to recognize SARS-CoV-2 from Indonesia, other five continents, as well as five VOCs, including the new Omicron sub-variant.

Clinical Evaluation of Direct Reverse Transcription PCR for Detection of SARS-CoV-2 Compared to Conventional RT-PCR in Patients with Positive Rapid Antigen Test Results during Circulation of Emerging Viral Variants

The emergence of the Omicron (B.1.1.529) variant of SARS-CoV-2 has precipitated a new global wave of the COVID-19 pandemic. The rapid identification of SARS-CoV-2 infection is imperative for the effective mitigation of transmission. Diagnostic modalities such as rapid antigen testing and real-time reverse transcription polymerase chain reaction (RT-PCR) offer expedient turnaround times of 10-15 min and straightforward implementation. This preliminary study assessed the correlation between outcomes of commercially available rapid antigen tests for home use and conventional reverse transcription polymerase chain reaction (RT-PCR) assays using a limited set of clinical specimens. Patients aged 5-99 years presenting to the emergency department for SARS-CoV-2 testing were eligible for enrollment (n = 5652). Direct PCR and conventional RT-PCR were utilized for the detection of SARS-CoV-2. The entire cohort of 5652 clinical specimens was assessed by both modalities to determine the clinical utility of the direct RT-PCR assay. Timely confirmation of SARS-CoV-2 infection may attenuate viral propagation and guide therapeutic interventions. Additionally, direct RT-PCR as a secondary confirmatory test for at-home rapid antigen test results demonstrated sensitivity comparable to conventional RT-PCR, indicating utility for implementation in laboratories globally, especially in resource-limited settings with constraints on reagents, equipment, and skilled personnel. In summary, direct RT-PCR enables the detection of SARS-CoV-2 with a sensitivity approaching that of conventional RT-PCR while offering expedient throughput and shorter turnaround times. Moreover, direct RT-PCR provides an open-source option for diagnostic laboratories worldwide, particularly in low- and middle-income countries.

Long COVID or Post-COVID-19 Condition: Past, Present and Future Research Directions

The presence of symptoms after an acute SARS-CoV-2 infection (long-COVID) has become a worldwide healthcare emergency but remains underestimated and undertreated due to a lack of recognition of the condition and knowledge of the underlying mechanisms. In fact, the prevalence of post-COVID symptoms ranges from 50% during the first months after the infection up to 20% two-years after. This perspective review aimed to map the existing literature on post-COVID symptoms and to identify gaps in the literature to guide the global effort toward an improved understanding of long-COVID and suggest future research directions. There is a plethora of symptomatology that can be due to COVID-19; however, today, there is no clear classification and definition of this condition, termed long-COVID or post-COVID-19 condition. The heterogeneity in the symptomatology has led to the presence of groups/clusters of patients, which could exhibit different risk factors and different mechanisms. Viral persistence, long-lasting inflammation, immune dysregulation, autoimmune reactions, reactivation of latent infections, endothelial dysfunction and alteration in gut microbiota have been proposed as potential mechanisms explaining the complexity of long-COVID. In such an equation, viral biology (e.g., re-infections, SARS-CoV-2 variants), host biology (e.g., genetics, epigenetics) and external factors (e.g., vaccination) should be also considered. These various factors will be discussed in the current perspective review and future directions suggested.

Surveillance of SARS-CoV-2 immunogenicity: loss of immunodominant HLA-A*02-restricted epitopes that activate CD8+ T cells

Introduction and methods

In this present work, coronavirus subfamilies and SARS-CoV-2 Variants of Concern (VOCs) were investigated for the presence of MHC-I immunodominant viral peptides using in silico and in vitro tools.

Results

In our results, HLA-A*02 haplotype showed the highest number of immunodominant epitopes but with the lowest combined prediction score. Furthermore, a decrease in combined prediction score was observed for HLA-A*02-restricted epitopes when the original strain was compared to the VOCs, indicating that the mutations on the VOCs are promoting escape from HLA-A2-mediated antigen presentation, which characterizes a immune evasion process. Additionally, epitope signature analysis revealed major immunogenic peptide loss for structural (S) and non-structural (ORF8) proteins of VOCs in comparison to the Wuhan sequence.

Discussion

These results may indicate that the antiviral CD8+ T-cell responses generated by original strains could not be sufficient for clearance of variants in either newly or reinfection with SARS-CoV-2. In contrast, N epitopes remain the most conserved and reactive peptides across SARS-CoV-2 VOCs. Overall, our data could contribute to the rational design and development of new vaccinal platforms to induce a broad cellular CD8+ T cell antiviral response, aiming at controlling viral transmission of future SARS-CoV-2 variants.

Role of available COVID-19 vaccines in reducing deaths and perspective for next generation vaccines and therapies to counter emerging viral variants: an update

The COVID-19 disease wreaked havoc all over the world causing more than 6 million deaths out of over 519 million confirmed cases. It not only disturbed the human race health-wise but also caused huge economic losses and social disturbances. The utmost urgency to counter pandemic was to develop effective vaccines as well as treatments that could reduce the incidences of infection, hospitalization and deaths. The most known vaccines that could help in managing these parameters are Oxford-AstraZeneca (AZD1222), Pfizer-BioNTech (BNT162b2), Moderna (mRNA-1273) and Johnson & Johnson (Ad26.COV2.S). The effectiveness of AZD1222 vaccine in reducing deaths is 88% in the age group 40-59 years, touching 100% in the age group 16-44 years & 65-84 years. BNT162b2 vaccine also did well in reducing deaths due to COVID-19 (95% in the age group 40-49 years and 100% in the age group 16-44 years. Similarly, mRNA-1273 vaccine showed potential in reducing COVID-19 deaths with effectiveness ranging from 80.3 to 100% depending upon age group of the vaccinated individuals. Ad26.COV2.S vaccine was also 100% effective in reducing COVID-19 deaths. The SARS-CoV-2 emerging variants have emphasized the need of booster vaccine doses to enhance protective immunity in vaccinated individuals. Additionally, therapeutic effectiveness of Molnupiravir, Paxlovid and Evusheld are also providing resistance against the spread of COVID-19 disease as well as may be effective against emerging variants. This review highlights the progress in developing COVID-19 vaccines, their protective efficacies, advances being made to design more efficacious vaccines, and presents an overview on advancements in developing potent drugs and monoclonal antibodies for countering COVID-19 and emerging variants of SARS-CoV-2 including the most recently emerged and highly mutated Omicron variant.

Precision management of post-COVID pain: An evidence and clinical-based approach

Background Pain after a SARS-CoV-2 acute infection (post-COVID pain) is becoming a new healthcare emergency but remains underestimated and most likely undertreated due to a lack of recognition of the phenomenon and knowledge of the underlying pain mechanisms. Evidence supporting any particular treatment approach for the management of post-COVID pain is lacking. Large variability in the patient response to any standard pain treatments is clinically observed, which has led to calls for a personalized, tailored approach to treating patients with chronic post-COVID pain (i.e. 'precision pain medicine'). Applying the global concerted action towards precision medicine to post-COVID pain could help guide clinical decision-making and aid in more effective treatments. Methods The current position paper discusses factors to be considered by clinicians for managing post-COVID pain ranging from identification of the pain phenotype to genetic consideration. Results The ability of clinicians to phenotype post-COVID pain into nociceptive, neuropathic, nociplastic or mixed type is suggested as the first step to better planification of a treatment programme. Further, the consideration of other factors, such as gender, comorbidities, treatments received at the acute phase of infection for onset-associated COVID-19 symptoms, factors during hospitalization or the presence of emotional disturbances should be implemented into a treatment programme. Conclusions Accordingly, considering these factors, management of post-COVID pain should include multimodal pharmacological and non-pharmacological modalities targeting emotional/cognitive aspects (i.e. psychological and/or coping strategies), central sensitization-associated mechanisms (i.e. pain neuroscience education), exercise programmes as well as lifestyle interventions (e.g. nutritional support and sleep management). SIGNIFICANCE: This position paper presents an evidence-based clinical reasoning approach for precision management of post-COVID pain.

Impact of Age and Variant Time Period on Clinical Presentation and Outcomes of Hospitalized Coronavirus Disease 2019 Patients

Objective

To evaluate the impact of age and COVID-19 variant time period on morbidity and mortality among those hospitalized with COVID-19.

Patients and Methods

Patients from the American Heart Association's Get With The Guidelines COVID-19 cardiovascular disease registry (January 20, 2020-February 14, 2022) were divided into groups based on whether they presented during periods of wild type/alpha, delta, or omicron predominance. They were further subdivided by age (young: 18-40 years; older: more than 40 years), and characteristics and outcomes were compared.

Results

The cohort consisted of 45,421 hospitalized COVID-19 patients (wild type/alpha period: 41,426, delta period: 3349, and omicron period: 646). Among young patients (18-40 years), presentation during delta was associated with increased odds of severe COVID-19 (OR, 1.6; 95% CI, 1.3-2.1), major adverse cardiovascular events (MACE) (OR, 1.8; 95% CI, 1.3-2.5), and in-hospital mortality (OR, 2.2; 95% CI, 1.5-3.3) when compared with presentation during wild type/alpha. Among older patients (more than 40 years), presentation during delta was associated with increased odds of severe COVID-19 (OR, 1.2; 95% CI, 1.1-1.3), MACE (OR, 1.5; 95% CI, 1.4-1.7), and in-hospital mortality (OR, 1.4; 95% CI, 1.3-1.6) when compared with wild type/alpha. Among older patients (more than 40 years), presentation during omicron associated with decreased odds of severe COVID-19 (OR, 0.7; 95% CI, 0.5-0.9) and in-hospital mortality (OR, 0.6; 95% CI, 0.5-0.9) when compared with wild type/alpha.

Conclusion

Among hospitalized adults with COVID-19, presentation during a time of delta predominance was associated with increased odds of severe COVID-19, MACE, and in-hospital mortality compared with presentation during wild type/alpha. Among older patients (aged more than 40 years), presentation during omicron was associated with decreased odds of severe COVID-19 and in-hospital mortality compared with wild type/alpha.

Genomic analysis of SARS-CoV-2 variants: diagnosis and vaccination challenges

SARS-CoV-2 put a heavy financial burden on the healthcare system, with millions of laboratory-confirmed cases and deaths worldwide in the last 2 years. During the seventh wave of this pandemic, the continuously evolving nature of SARS-CoV-2 resulted in the emergence of new variants that harbor different mutations. Mutations are associated with changes in the virus behavior, including increased transmissibility, increased virulence, and evasion of neutralizing antibodies. Currently, we need detailed and comprehensive genomic information on all SARS-CoV-2 variants. One of the key points in this study was the genome survey of mutation profiles across variants as a genomic data source, to determine the efficiency of RT-qPCR assays. We also used the source to calculate the binding affinity changes of neutralizing antibodies-mutant receptor binding domain (RBD) complexes and determine vaccine efficacy. Our result revealed that the number of nucleotide mismatches is variable in the WHO-recommended primer-probe sets. Mismatches located at the 3' ends of the oligonucleotide, may lead to false-negative results. Only the primer-probe sets designed by the Ministry of Public Health of Thailand were exclusive and cannot detect the omicron variant reliably. Binding affinity changes showed that E484K was more deleterious than other mutations and decreased stability between the mutant RBD protein and neutralizing antibodies. The Omicrons show the highest change in binding affinity which may lead to immune escape and increase transmissibility. Additionally, the 7D6 monoclonal antibody in the 7eam complex could neutralize all variants of SARS-CoV-2. We strongly recommend creating and improving a matrix accuracy by processing a large number of SARS-CoV-2 sequences to update RT-qPCR assays and identified immunogenic residues among conserved RBD. Also, a detail computational analysis is needed to investigate distinctive amino acid substitution patterns which may be foundational in the vaccines. Finally, designing in-vitro studies can help confirm the present study and manage COVID-19 patients.Communicated by Ramaswamy H. Sarma.

Impact of CoronaVac on Covid-19 outcomes of elderly adults in a large and socially unequal Brazilian city: A target trial emulation study

BACKGROUND

Although CoronaVac was the only Covid-19 vaccine adopted in the first months of the Brazilian vaccination campaign, randomized clinical trials to evaluate its efficacy in elderly adults were limited. In this study, we use routinely collected surveillance and SARS-CoV-2 vaccination and testing data comprising the population of the fifth largest city of Brazil to evaluate the effectiveness of CoronaVac in adults 60+ years old against severe outcomes.

METHODS

Using large observational databases on vaccination and surveillance data from the city of Fortaleza, Brazil, we defined a retrospective cohort including 324,302 eligible adults aged ≥60 years to evaluate the effectiveness of the CoronaVac vaccine. The cohort included individuals vaccinated between January 21, 2021, and August 31, 2021, who were matched with unvaccinated persons at the time of rollout following a 1:1 ratio according to baseline covariates of age, sex, and Human Development Index of the neighborhood of residence. Only Covid-19-related severe outcomes were included in the analysis: hospitalization, ICU admission, and death. Vaccine effectiveness for each outcome was calculated by using the risk ratio between the two groups, with the risk obtained by the Kaplan-Meier estimator.

RESULTS

We obtained 62,643 matched pairs for assessing the effectiveness of the two-dose regimen of CoronaVac. The demographic profile of the matched population was statistically representative of the population of Fortaleza. Using the cumulative incidence as the risk associated with each group, starting at day 14 since the receipt of the second dose, we found an 82.3 % (95 % CI 66.3-93.9) effectiveness against Covid-19-related death, 68.4 % (95 % CI 42.3-86.4) against ICU admission, and 55.8 % (95 % CI 42.7-68.3) against hospital admission.

CONCLUSIONS

Our results show that, despite critical delays in vaccine delivery and limited evidence in efficacy trial estimates, CoronaVac contributed to preventing deaths and severe morbidity due to Covid-19 in elderly adults.

Identification of inhibitors against SARS-CoV-2 variants of concern using virtual screening and metadynamics-based enhanced sampling

Among the variants of SARS-CoV-2, some are more infectious than the Wild-type. Interestingly, these mutations enable the virus to evade the therapeutic efforts. Hence, there is a need for candidate drug molecules that can potently bind with all the variants. We have adopted a strategy combining virtual screening, molecular docking followed by rigorous sampling by metadynamics simulations to find candidate molecules. From our results we found four highly potent drug candidates that can bind to the Spike-RBD of all the variants of the virus. Additionally, we also found that certain signature residues on the RBM region commonly bind to each of these inhibitors. Thus, our study not only gives information on the chemical compounds, but also residues on the proteins which could be targeted for future drug and vaccine development studies.

Molecular and Clinical Epidemiology of SARS-CoV-2 Infection among Vaccinated and Unvaccinated Individuals in a Large Healthcare Organization from New Jersey

New Jersey was among the first states impacted by the COVID-19 pandemic, with one of the highest overall death rates in the nation. Nevertheless, relatively few reports have been published focusing specifically on New Jersey. Here we report on molecular, clinical, and epidemiologic observations, from the largest healthcare network in the state, in a cohort of vaccinated and unvaccinated individuals with laboratory-confirmed SARS-CoV-2 infection. We conducted molecular surveillance of SARS-CoV-2-positive nasopharyngeal swabs collected in nine hospitals from December 2020 through June 2022, using both whole genome sequencing (WGS) and a real-time RT-PCR screening assay targeting spike protein mutations found in variants of concern (VOCs) within our region. De-identified clinical data were obtained retrospectively, including demographics, COVID-19 vaccination status, ICU admission, ventilator support, mortality, and medical history. Statistical analyses were performed to identify associations between SARS-CoV-2 variants, vaccination status, clinical outcomes, and medical risk factors. A total of 5007 SARS-CoV-2-positive nasopharyngeal swabs were successfully screened and/or sequenced. Variant screening identified three predominant VOCs, including Alpha (n = 714), Delta (n = 1877), and Omicron (n = 1802). Omicron isolates were further sub-typed as BA.1 (n = 899), BA.2 (n = 853), or BA.4/BA.5 (n = 50); the remaining 614 isolates were classified as "Other". Approximately 31.5% (1577/5007) of the samples were associated with vaccine breakthrough infections, which increased in frequency following the emergence of Delta and Omicron. Severe clinical outcomes included ICU admission (336/5007 = 6.7%), ventilator support (236/5007 = 4.7%), and mortality (430/5007 = 8.6%), with increasing age being the most significant contributor to each (p < 0.001). Unvaccinated individuals accounted for 79.7% (268/336) of ICU admissions, 78.3% (185/236) of ventilator cases, and 74.4% (320/430) of deaths. Highly significant (p < 0.001) increases in mortality were observed in individuals with cardiovascular disease, hypertension, cancer, diabetes, and hyperlipidemia, but not with obesity, thyroid disease, or respiratory disease. Significant differences (p < 0.001) in clinical outcomes were also noted between SARS-CoV-2 variants, including Delta, Omicron BA.1, and Omicron BA.2. Vaccination was associated with significantly improved clinical outcomes in our study, despite an increase in breakthrough infections associated with waning immunity, greater antigenic variability, or both. Underlying comorbidities contributed significantly to mortality in both vaccinated and unvaccinated individuals, with increasing risk based on the total number of comorbidities. Real-time RT-PCR-based screening facilitated timely identification of predominant variants using a minimal number of spike protein mutations, with faster turnaround time and reduced cost compared to WGS. Continued evolution of SARS-CoV-2 variants will likely require ongoing surveillance for new VOCs, with real-time assessment of clinical impact.

ACE2 receptor polymorphism in humans and animals increases the risk of the emergence of SARS-CoV-2 variants during repeated intra- and inter-species host-switching of the virus

Like other coronaviruses, SARS-CoV-2 has ability to spread through human-to-human transmission and to circulate from humans to animals and from animals to humans. A high frequency of SARS-CoV-2 mutations has been observed in the viruses isolated from both humans and animals, suggesting a genetic fitness under positive selection in both ecological niches. The most documented positive selection force driving SARS-CoV-2 mutations is the host-specific immune response. However, after electrostatic interactions with lipid rafts, the first contact between the virus and host proteins is the viral spike-cellular receptor binding. Therefore, it is likely that the first level of selection pressure impacting viral fitness relates to the virus's affinity for its receptor, the angiotensin I converting enzyme 2 (ACE2). Although sufficiently conserved in a huge number of species to support binding of the viral spike with enough affinity to initiate fusion, ACE2 is highly polymorphic both among species and within a species. Here, we provide evidence suggesting that when the viral spike-ACE2 receptor interaction is not optimal, due to host-switching, mutations can be selected to improve the affinity of the spike for the ACE2 expressed by the new host. Notably, SARS-CoV-2 is mutation-prone in the spike receptor binding domain (RBD), allowing a better fit for ACE2 orthologs in animals. It is possibly that this may also be true for rare human alleles of ACE2 when the virus is spreading to billions of people. In this study, we present evidence that human subjects expressing the rare E₃₂₉G allele of ACE2 with higher allele frequencies in European populations exhibit a improved affinity for the SARS-CoV-2 spike N₅₀₁Y variant of the virus. This may suggest that this viral N₅₀₁Y variant emerged in the human population after SARS-CoV-2 had infected a human carrying the rare E₃₂₉G allele of ACE2. In addition, this viral evolution could impact viral replication as well as the ability of the adaptive humoral response to control infection with RBD-specific neutralizing antibodies. In a shifting landscape, this ACE2-driven genetic drift of SARS-CoV-2 which we have named the 'boomerang effect', could complicate the challenge of preventing COVID with a SARS-CoV-2 spike-derived vaccine.

Rapid detection of intact SARS-CoV-2 using designer DNA Nets and a pocket-size smartphone-linked fluorimeter

Rapid, sensitive, and inexpensive point-of-care diagnosis is vital to controlling highly infectious diseases, including COVID-19. Here, we report the design and characterization of a compact fluorimeter called a "Virus Pod" (V-Pod) that enables sensitive self-testing of SARS-CoV-2 viral load in saliva. The rechargeable battery-operated device reads the fluorescence generated by Designer DNA Nanostructures (DDN) when they specifically interact with intact SARS-CoV-2 virions. DDNs are net-shaped self-assembling nucleic acid constructs that provide an array of highly specific aptamer-fluorescent quencher duplexes located at precise positions that match the pattern of spike proteins. The room-temperature assay is performed by mixing the test sample with DNA Net sensor in a conventional PCR tube and placing the tube into the V-Pod. Fluorescent signals are generated when multivalent aptamer-spike binding releases fluorescent quenchers, resulting in rapid (5-min) generation of dose-dependent output. The V-Pod instrument performs laser excitation, fluorescence intensity quantitation, and secure transmission of data to an App via Bluetooth™. We show that the V-Pod and DNA Net assay achieves clinically relevant detection limits of 3.92 × 103 viral-genome-copies/mL for pseudo-typed wild-type SARS-CoV-2 and 1.84 × 104, 9.69 × 104, 6.99 × 104 viral-genome-copies/mL for pathogenic Delta, Omicron, and D614G variants, representing sensitivity similar to laboratory-based PCR. The pocket-sized instrument (∼$294), inexpensive reagent-cost/test ($1.26), single-step, rapid sample-to-answer, and quantitative output represent a capability that is compatible with the needs of frequent self-testing in a consumer-friendly format that can link with medical service systems such as healthcare providers, contact tracing, and infectious disease reporting.

Development of SARS-CoV-2 Vaccine: Challenges and Prospects

The WHO declared coronavirus disease 2019 (COVID-19) a pandemic in March 2020, which was caused by novel coronavirus severe acute respiratory coronavirus 2 (SARS-CoV-2). SARS-CoV-2 made its first entry into the world in November 2019, and the first case was detected in Wuhan, China. Mutations in the SARS-CoV-2 genome distressed life in almost every discipline by the extended production of novel viral variants. In this article, authorized SARS-CoV-2 vaccines including mRNA vaccines, DNA vaccines, subunit vaccines, inactivated virus vaccines, viral vector vaccine, live attenuated virus vaccines and mix and match vaccines will be discussed based on their mechanism, administration, storage, stability, safety and efficacy. The information was collected from various journals via electronic searches including PubMed, Science Direct, Google Scholar and the WHO platform. This review article includes a brief summary on the pathophysiology, epidemiology, mutant variants and management strategies related to COVID-19. Due to the continuous production and unsatisfactory understanding of novel variants of SARS-CoV-2, it is important to design an effective vaccine along with long-lasting protection against variant strains by eliminating the gaps through practical and theoretical knowledge. Consequently, it is mandatory to update the literature through previous and ongoing trials of vaccines tested among various ethnicities and age groups to gain a better insight into management strategies and combat complications associated with upcoming novel variants of SARS-CoV-2.

Next-generation nanophotonic-enabled biosensors for intelligent diagnosis of SARS-CoV-2 variants

Constantly mutating SARS-CoV-2 is a global concern resulting in COVID-19 infectious waves from time to time in different regions, challenging present-day diagnostics and therapeutics. Early-stage point-of-care diagnostic (POC) biosensors are a crucial vector for the timely management of morbidity and mortalities caused due to COVID-19. The state-of-the-art SARS-CoV-2 biosensors depend upon developing a single platform for its diverse variants/biomarkers, enabling precise detection and monitoring. Nanophotonic-enabled biosensors have emerged as 'one platform' to diagnose COVID-19, addressing the concern of constant viral mutation. This review assesses the evolution of current and future variants of the SARS-CoV-2 and critically summarizes the current state of biosensor approaches for detecting SARS-CoV-2 variants/biomarkers employing nanophotonic-enabled diagnostics. It discusses the integration of modern-age technologies, including artificial intelligence, machine learning and 5G communication with nanophotonic biosensors for intelligent COVID-19 monitoring and management. It also highlights the challenges and potential opportunities for developing intelligent biosensors for diagnosing future SARS-CoV-2 variants. This review will guide future research and development on nano-enabled intelligent photonic-biosensor strategies for early-stage diagnosing of highly infectious diseases to prevent repeated outbreaks and save associated human mortalities.

Epitope-directed anti-SARS-CoV-2 scFv engineered against the key spike protein region could block membrane fusion

The newly emerged SARS-CoV-2 causing coronavirus disease (COVID-19) resulted in >500 million infections. A great deal about the molecular processes of virus infection in the host is getting uncovered. Two sequential proteolytic cleavages of viral spike protein by host proteases are prerequisites for the entry of the virus into the host cell. The first cleavage occurs at S1/S2 site by the furin protease, and the second cleavage at a fusion activation site, the S2' site, by the TMPRSS2 protease. S2' cleavage site is present in the S2 domain of spike protein followed by a fusion peptide. Given the S2' site to be conserved among all the SARS-CoV-2 variants, we chose an S2' epitope encompassing the S2' cleavage site and generated single-chain antibodies (scFvs) through an exhaustive phage display library screening. Crystal structure of a scFv in complex with S2' epitope was determined. Incidentally, S2' epitope in the scFv bound structure adopts an alpha-helical conformation equivalent to the conformation of the epitope in the spike protein. Furthermore, these scFvs can bind to the spike protein expressed either in vitro or on the mammalian cell surface. We illustrate a molecular model based on structural and biochemical insights into the antibody-S2' epitope interaction emphasizing scFvs mediated blocking of virus entry into the host cell by restricting the access of TMPRSS2 protease and consequently inhibiting the S2' cleavage competitively.

Dynamics of Different Classes and Subclasses of Antibody Responses to Severe Acute Respiratory Syndrome Coronavirus 2 Variants after Coronavirus Disease 2019 and CoronaVac Vaccination in Thailand

The humoral immune response plays a key role in protecting the population from SARS-CoV-2 transmission. Patients who recovered from COVID-19 as well as fully vaccinated individuals have elevated levels of antibodies. The dynamic levels of the classes and subclasses of antibody responses to new variants that occur in different populations remain unclear. We prospectively recruited 60 participants, including COVID-19 patients and CoronaVac-vaccinated individuals, in Thailand from May to August 2021. Plasma samples were collected on day 0, day 14, and day 28 to determine the dynamic levels of the classes and subclasses of plasma antibodies against the receptor-binding domain (RBD) in the spike protein (S) of four SARS-CoV-2 strains (Wuhan, Alpha, Delta, and Omicron) via enzyme-linked immunosorbent assay. Our results indicated that the patients with SARS-CoV-2 infections had broader class and subclass profiles as well as higher levels of anti-S RBD antibodies to the Wuhan, Alpha, and Delta strains than did the CoronaVac-vaccinated individuals. The median antibody levels increased and subsequently declined in a month in the COVID-19 patients and in the vaccinated group. Correlations of the classes and subclasses of antibodies were observed in the COVID-19 patients but not in the vaccinated individuals. The levels of all of the anti-S RBD antibodies against the Omicron variant were low in the patients and in the vaccinated individuals. Our study revealed distinct antibody profiles between the two cohorts, suggesting different pathways of immune activation. This could have an impact on protection from infections by new variants of concern (VOC). IMPORTANCE The antibody responses to new SARS-CoV-2 variants that occur in different populations remain unclear. In this study, we recruited 60 participants, including COVID-19 patients and CoronaVac-vaccinated individuals, in Thailand and determined the dynamic levels of the IgG, IgA, IgM, and IgG subclasses of antibodies against the spike protein (S) of four SARS-CoV-2 strains. Our results showed that the patients with SARS-CoV-2 infections had broader profiles and higher levels of antibodies to the Wuhan, Alpha, and Delta strains than did the CoronaVac-vaccinated individuals. The antibody levels of both groups increased and subsequently decreased within 1 month. Higher and functional correlations of these antibodies were observed in the COVID-19 patients. The levels of all anti-S RBD antibodies against the Omicron variant were low in patients and vaccinated individuals. Our study revealed distinct antibody responses between the two groups, suggesting different pathways of immune response, which may have an impact on protection from infections by new SARS-CoV-2 variants.

Comparison of antibody responses before and after booster doses with the Pfizer-BioNTech or Oxford-AstraZeneca vaccines in healthcare workers in Thailand

The severe acute respiratory syndrome 2 (SARS-CoV-2) has spread rapidly worldwide, not only causing significant morbidity and mortality but also dramatically increasing health care spending. To manage this in Thailand, healthcare workers first received two doses of the CoronaVac vaccine followed by a booster vaccine with either BNT162b2 vaccine (Pfizer-BioNTech; PZ) or ChAdOx1 nCoV-19 vaccine (Oxford-AstraZeneca; AZ). Given that the difference in anti-SARS-CoV-2 levels following vaccination may vary depending on the vaccine and on demographic characteristics, we measured the antibody response after the second CoronaVac dose and after the booster with either the PZ or AZ vaccine. Our results in 473 healthcare workers show that the variation in antibody response to the full CoronaVac dose depends on demographic characteristics such as age, gender, body mass index, and underlying disease. After receiving a booster dose, anti-SARS-CoV-2 levels were significantly higher in participants who received the PZ vaccine than in people who received the AZ vaccine. Overall, however, receiving a booster dose of either the PZ or AZ vaccine promoted strong antibody responses, even in the old and those with obesity or diabetes mellitus. In conclusion, our results support the use of a booster vaccination program after full vaccination with the CoronaVac vaccine. This approach effectively enhances immunity against SARS-CoV-2, especially in clinically vulnerable groups and healthcare workers.

More or less deadly? A mathematical model that predicts SARS-CoV-2 evolutionary direction

SARS-CoV-2 has caused tremendous deaths globally. It is of great value to predict the evolutionary direction of SARS-CoV-2. In this paper, we proposed a novel mathematical model that could predict the evolutionary trend of SARS-CoV-2. We focus on the mutational effects on viral assembly capacity. A robust coarse-grained mathematical model is constructed to simulate the virus dynamics in the host body. Both virulence and transmissibility can be quantified in this model. A delicate equilibrium point that optimizes the transmissibility can be numerically obtained. Based on this model, the virulence of SARS-CoV-2 might further decrease, accompanied by an enhancement of transmissibility. However, this trend is not continuous; its virulence will not disappear but remains at a relatively stable range. A virus assembly model which simulates the virus packing process is also proposed. It can be explained why a few mutations would lead to a significant divergence in clinical performance, both in the overall particle formation quantity and virulence. This research provides a novel mathematical attempt to elucidate the evolutionary driving force in RNA virus evolution.

Headache as a COVID-19 onset symptom or Post-COVID symptom according to the SARS-CoV-2 Variant

INTRODUCTION

COVID19 associated headaches are highly common and there is currently an unmet need to better understand their association with SARSCoV2 variants. Headaches are a prevalent symptom in the acute phase of COVID19 and are associated with a better prognosis and better immune response. They are also a relevant post-COVID symptom.

AREAS COVERED

This article analyses the differences in the prevalence of headache as an onset symptom and in post-COVID headache among the different SARS-CoV-2 variants: the historical strain, Alpha, Delta and Omicron. The different pathophysiological mechanisms by which SARS-CoV-2 infection may cause headache are also discussed.

EXPERT OPINION

The presence of headache at the acute phase is a risk factor for post-COVID headache, whereas a history of primary headache does not appear to be associated with post-COVID headache. The prevalence of headache as an onset symptom appears to be variable for the different SARS-CoV-2 variants, but current data are inconclusive. However, the current evidence also suggests that headache represents a prevalent symptom in the acute and post-infection COVID-19 phase, regardless of SARS-CoV-2 variant.

A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies

The COVID-19 pandemic has created significant concern for everyone. Recent data from many worldwide reports suggest that most infections are caused by the Omicron variant and its sub-lineages, dominating all the previously emerged variants. The numerous mutations in Omicron's viral genome and its sub-lineages attribute it a larger amount of viral fitness, owing to the alteration of the transmission and pathophysiology of the virus. With a rapid change to the viral structure, Omicron and its sub-variants, namely BA.1, BA.2, BA.3, BA.4, and BA.5, dominate the community with an ability to escape the neutralization efficiency induced by prior vaccination or infections. Similarly, several recombinant sub-variants of Omicron, namely XBB, XBD, and XBF, etc., have emerged, which a better understanding. This review mainly entails the changes to Omicron and its sub-lineages due to it having a higher number of mutations. The binding affinity, cellular entry, disease severity, infection rates, and most importantly, the immune evading potential of them are discussed in this review. A comparative analysis of the Delta variant and the other dominating variants that evolved before Omicron gives the readers an in-depth understanding of the landscape of Omicron's transmission and infection. Furthermore, this review discusses the range of neutralization abilities possessed by several approved antiviral therapeutic molecules and neutralizing antibodies which are functional against Omicron and its sub-variants. The rapid evolution of the sub-variants is causing infections, but the broader aspect of their transmission and neutralization has not been explored. Thus, the scientific community should adopt an elucidative approach to obtain a clear idea about the recently emerged sub-variants, including the recombinant variants, so that effective neutralization with vaccines and drugs can be achieved. This, in turn, will lead to a drop in the number of cases and, finally, an end to the pandemic.

Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies

Newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are continuously posing high global public health concerns and panic resulting in waves of coronavirus disease 2019 (COVID-19) pandemic. Depending on the extent of genomic variations, mutations and adaptation, few of the variants gain the ability to spread quickly across many countries, acquire higher virulency and ability to cause severe disease, morbidity and mortality. These variants have been implicated in lessening the efficacy of the current COVID-19 vaccines and immunotherapies resulting in break-through viral infections in vaccinated individuals and recovered patients. Altogether, these could hinder the protective herd immunity to be achieved through the ongoing progressive COVID-19 vaccination. Currently, the only variant of interest of SARS-CoV-2 is Omicron that was first identified in South Africa. In this review, we present the overview on the emerging SARS-CoV-2 variants with a special focus on the Omicron variant, its lineages and hybrid variants. We discuss the hypotheses of the origin, genetic change and underlying molecular mechanism behind higher transmissibility and immune escape of Omicron variant. Major concerns related to Omicron including the efficacy of the current available immunotherapeutics and vaccines, transmissibility, disease severity, and mortality are discussed. In the last part, challenges and strategies to counter Omicron variant, its lineages and hybrid variants amid the ongoing COVID-19 pandemic are presented.

The COVID-19 Pandemic: SARS-CoV-2 Structure, Infection, Transmission, Symptomology, and Variants of Concern

Since it was first detected in December 2019, the COVID-19 pandemic has spread across the world and affected virtually every country and territory. The pathogen driving this pandemic is SARS-CoV-2, a positive-sense single-stranded RNA virus which is primarily transmissible though the air and can cause mild to severe respiratory infections in humans. Within the first year of the pandemic, the situation worsened with the emergence of several SARS-CoV-2 variants. Some of these were observed to be more virulent with varying capacities to escape the existing vaccines and were, therefore, denoted as variants of concern. This chapter provides a general overview of the course of the COVID-19 pandemic up to April 2022 with a focus on the structure, infection, transmission, and symptomology of the SARS-CoV-2 virus. The main objectives were to investigate the effects of the variants of concern on the trajectory of the virus and to highlight a potential pathway for coping with the current and future pandemics.

Cross-immunity against SARS-COV-2 variants of concern in naturally infected critically ill COVID-19 patients

Critically ill patients infected with SARS-CoV-2 display adaptive immunity, but it is unknown if they develop cross-reactivity to variants of concern (VOCs). We profiled cross-immunity against SARS-CoV-2 VOCs in naturally infected, non-vaccinated, critically ill COVID-19 patients. Wave-1 patients (wild-type infection) were similar in demographics to Wave-3 patients (wild-type/alpha infection), but Wave-3 patients had higher illness severity. Wave-1 patients developed increasing neutralizing antibodies to all variants, as did patients during Wave-3. Wave-3 patients, when compared to Wave-1, developed more robust antibody responses, particularly for wild-type, alpha, beta and delta variants. Within Wave-3, neutralizing antibodies were significantly less to beta and gamma VOCs, as compared to wild-type, alpha and delta. Patients previously diagnosed with cancer or chronic obstructive pulmonary disease had significantly fewer neutralizing antibodies. Naturally infected ICU patients developed adaptive responses to all VOCs, with greater responses in those patients more likely to be infected with the alpha variant, versus wild-type.

Strategies to tackle SARS-CoV-2 Mu, a newly classified variant of interest likely to resist currently available COVID-19 vaccines

Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have recently been reported in many countries. These have exacerbated the coronavirus disease 2019 (COVID-19)-induced global health threats and hindered COVID-19 vaccine development and therapeutic progress. This commentary discusses the potential risk of the newly classified Mu variant of interest, seeming a highly vaccine-resistant variant, and the approaches that can be adopted to tackle this variant based on the available evidence. The SARS-CoV-2 B.1.621 (Mu variant) lineage has shown approximately ten times higher resistance to neutralizing sera obtained from COVID-19 survivors or BNT161b2-vaccinated people than the parenteral B.1 lineage. Several urgent and long-term strategic plans, including quick genomic surveillance for uncovering the genetic characteristics of the variants, equitable global mass vaccination, booster dose administration if required, and strict implementation of public health measures or non-pharmaceutical interventions, must be undertaken concertedly to restrict further infections, mutations, or recombination of the SARS-CoV-2 virus and its deadly strains.

Characterization and Function of Glycans on the Spike Proteins of SARS-CoV-2 Variants of Concern

SARS-CoV-2 variants of concern (VOCs) pose a great challenge to viral prevention and treatment owing to spike (S) protein mutations, which enhance their infectivity and capacity for immune evasion. However, whether these S protein mutations affect glycosylation patterns and thereby influence infectivity and immunogenicity remains unclear. In this study, four VOC S proteins-S-Alpha, S-Beta, S-Delta, and S-Omicron-were expressed and purified. Lectin microarrays were performed to characterize their glycosylation patterns. Several glycans were differentially expressed among the four VOC S proteins. Furthermore, the functional examination of glycans differentially expressed on S-Omicron revealed a higher expression of fucose-containing glycans, which modestly increased the binding of S-Omicron to angiotensin converting enzyme 2 (ACE2). A higher abundance of sialic acid and galactose-containing glycan was observed on S-Omicron, which significantly reduced its sensitivity against broad S protein-neutralizing antibodies. These findings contribute to the further understanding of SARS-CoV-2 infection mechanisms and provide novel glycan targets for emerging and future variants of SARS-CoV-2. IMPORTANCE Though glycosylation sites of SARS-CoV-2 S protein remain highly conserved, we confirmed that mutations in the Spike gene affect the S protein glycan expression pattern in different variants. More importantly, we found that glycans were differentially expressed on the S protein of the Omicron variant, enabling different forms of receptor binding and neutralization resistance. This study improves our understanding of SARS-CoV-2 glycomics and glycobiology and provides novel therapeutic and preventive strategies for SARS-CoV-2 VOCs.

SARS-CoV-2 whole-proteome sequences from environment as an indicator of community viral distribution, evolution and epidemiological dynamics: A cohort analysis of Austria

Several investigations have been carried out to detect SARS-CoV-2 samples from the environment such as sewage waters and surface swabs. Whole-proteome sequence analysis of 847 SARS-CoV-2 genome sequences collected from the environment in Austria during 2021 and deposited in GISAID indicates that alpha and delta are two dominant variants, coinciding with the human clinical samples with a Pearson correlation coefficient in the range of 0.58 (alpha variant) to 0.82 (delta variant). Both environmental and human samples show that Austrian SARS-CoV-2 alpha variant is found to possess N protein R203K and G204R/P mutations, whereas they are absent in the delta variant. SARS-CoV-2 delta variant is continuously seen in both the environmental and human clinical samples from the month of September 2021 and it spiked in November 2021, which is directly reflected in the increase of the number of SARS-CoV-2 infections and deaths in Austria during November 2021. Thus, the results presented here indicate that the environmental SARS-CoV-2 whole-genome sequences collected from Austria reflect the community viral distribution, evolution and the concomitant epidemiological dynamics. Since SARS-CoV-2 keeps evolving, the results presented here further suggest the need to monitor the environment for the early detection of SARS-CoV-2 variants to take appropriate precautionary measures.

Predicting the outcome for COVID-19 patients by applying time series classification to electronic health records

Background

COVID-19 caused more than 622 thousand deaths in Brazil. The infection can be asymptomatic and cause mild symptoms, but it also can evolve into a severe disease and lead to death. It is difficult to predict which patients will develop severe disease. There are, in the literature, machine learning models capable of assisting diagnose and predicting outcomes for several diseases, but usually these models require laboratory tests and/or imaging.

Methods

We conducted a observational cohort study that evaluated vital signs and measurements from patients who were admitted to Hospital das Clínicas (São Paulo, Brazil) between March 2020 and October 2021 due to COVID-19. The data was then represented as univariate and multivariate time series, that were used to train and test machine learning models capable of predicting a patient’s outcome.

Results

Time series-based machine learning models are capable of predicting a COVID-19 patient’s outcome with up to 96% general accuracy and 81% accuracy considering only the first hospitalization day. The models can reach up to 99% sensitivity (discharge prediction) and up to 91% specificity (death prediction).

Conclusions

Results indicate that time series-based machine learning models combined with easily obtainable data can predict COVID-19 outcomes and support clinical decisions. With further research, these models can potentially help doctors diagnose other diseases.

Efficacy and safety of integrated traditional Chinese and Western medicine against COVID-19: A systematic review and meta-analysis

Although plenty of clinical trials have confirmed the efficacy and safety of integrated traditional Chinese and Western medicine (ITCWM) against COVID-19, the role of ITCWM remains controversial. So we conducted a systematic review and meta-analysis of published studies in eight major databases that report the outcomes of interest in COVID-19 patients receiving ITCWM. RevMan5.4 software was used for meta-analysis, while the quality of RCTs was assessed by the Cochrane risk of bias tool and the retrospective studies were assessed by Newcastle-Ottawa Scale. Eventually, a total of 53 studies with 5425 COVID-19 patients was identified. The meta-analysis results showed that ITCWM was significantly better than western medicine treatment (WMT) alone in the percentage of cases changing to severe/critical [RR = 0.40, 95%CI (0.33, 0.49), p < .00001, I²  = 10%], overall clinical effectiveness [RR = 1.26, 95% CI (1.18, 1.35), p < .00001, I²  = 50%], time to defervescencer [MD = -1.45, 95% CI (-1.82, -1.07), p < .00001, I²  = 83%], disappearing time of cough [MD = -2.11, 95% CI (-2.98, -1.25), p < .00001, I²  = 93%], time of RT-PCR negativity [MD = -3.35, 95% CI (-4.74, -1.95), p < .00001, I²  = 92%], length of hospital stay [MD = -4.05, 95% CI (-5.24, -2.85), p < .00001, I²  = 91%], improvement in CT scan [RR = 1.22, 95% CI (1.17, 1.28), p < .00001, I²  = 46%], TCM syndrome score [MD = -3.95, 95% CI (-5.07, -2.82), p < .00001, I²  = 92%], disappearance rate of fever [RR = 1.23, 95% CI (1.10, 1.38), p < .00001, I²  = 85%], disappearance rate of cough [RR = 1.43, 95% CI (1.25, 1.63), p < .00001, I²  = 60%], level of CRP [MD = -9.23, 95% CI (-10.94, -7.52), p < .00001, I²  = 97%], and WBC [MD = -9.23, 95% CI (-10.94, -7.52), p < .00001, I²  = 97%]. There is no significant difference between ITCWM and WMT in the adverse reaction rate [RR = 0.85, 95% CI(0.71, 1.03), p = .10, I²  = 25%]. Our results showed evidence of clinical efficacy and safety benefit in COVID-19 patients treated with ITCWM. In spite of some limitations, the rapidly developing global pandemic warrants further high-quality and multicenter clinical studies to confirm the contribution of ITCWM.

Need of booster vaccine doses to counteract the emergence of SARS-CoV-2 variants in the context of the Omicron variant and increasing COVID-19 cases: An update

The emergence of different variants of SARS-CoV-2, including the Omicron (B.1.1.529) variant in November 2021, has resulted in a continuous major health concern at a global scale. Presently, the Omicron variant has spread very rapidly worldwide within a short time period. As the most mutated variant of SARS-CoV-2, Omicron has instilled serious uncertainties on the effectiveness of humoral adaptive immunity generated by COVID-19 vaccination or an active viral infection as well as the protection provided by antibody-based immunotherapies. Amidst such high public health concerns, the need to carry out booster vaccination has been emphasized. Current evidence reveals the importance of incorporating booster vaccination using several vaccine platforms, such as viral vector- and mRNA-based vaccines, as well as other platforms that are under explorative investigations. Further research is being conducted to assess the effectiveness and durability of protection provided by booster COVID-19 vaccination against Omicron and other SARS-CoV-2 variants.

Electrostatic Interactions Are the Primary Determinant of the Binding Affinity of SARS-CoV-2 Spike RBD to ACE2: A Computational Case Study of Omicron Variants

To explore the mechanistic origin that determines the binding affinity of SARS-CoV-2 spike receptor binding domain (RBD) to human angiotensin converting enzyme 2 (ACE2), we constructed the homology models of RBD-ACE2 complexes of four Omicron subvariants (BA.1, BA.2, BA.3 and BA.4/5), and compared them with wild type complex (RBD_WT-ACE2) in terms of various structural dynamic properties by molecular dynamics (MD) simulations and binding free energy (BFE) calculations. The results of MD simulations suggest that the RBDs of all the Omicron subvariants (RBD_OMIs) feature increased global structural fluctuations when compared with RBD_WT. Detailed comparison of BFE components reveals that the enhanced electrostatic attractive interactions are the main determinant of the higher ACE2-binding affinity of RBD_OMIs than RBD_WT, while the weakened electrostatic attractive interactions determine RBD of BA.4/5 subvariant (RBD_BA.4/5) lowest ACE2-binding affinity among all Omicron subvariants. The per-residue BFE decompositions and the hydrogen bond (HB) networks analyses indicate that the enhanced electrostatic attractive interactions are mainly through gain/loss of the positively/negatively charged residues, and the formation or destruction of the interfacial HBs and salt bridges can also largely affect the ACE2-binding affinity of RBD. It is worth pointing out that since Q493R plays the most important positive contribution in enhancing binding affinity, the absence of this mutation in RBD_BA.4/5 results in a significantly weaker binding affinity to ACE2 than other Omicron subvariants. Our results provide insight into the role of electrostatic interactions in determining of the binding affinity of SARS-CoV-2 RBD to human ACE2.

Long-COVID Symptoms in Individuals Infected with Different SARS-CoV-2 Variants of Concern: A Systematic Review of the Literature

The association of SARS-CoV-2 variants with long-COVID symptoms is still scarce, but new data are appearing at a fast pace. This systematic review compares the prevalence of long-COVID symptoms according to relevant SARS-CoV-2 variants in COVID-19 survivors. The MEDLINE, CINAHL, PubMed, EMBASE and Web of Science databases, as well as the medRxiv and bioRxiv preprint servers, were searched up to 25 October 2022. Case-control and cohort studies analyzing the presence of post-COVID symptoms appearing after an acute SARS-CoV-2 infection by the Alpha (B.1.1.7), Delta (B.1.617.2) or Omicron (B.1.1.529/BA.1) variants were included. Methodological quality was assessed using the Newcastle-Ottawa Scale. From 430 studies identified, 5 peer-reviewed studies and 1 preprint met the inclusion criteria. The sample included 355 patients infected with the historical variant, 512 infected with the Alpha variant, 41,563 infected with the Delta variant, and 57,616 infected with the Omicron variant. The methodological quality of all studies was high. The prevalence of long-COVID was higher in individuals infected with the historical variant (50%) compared to those infected with the Alpha, Delta or Omicron variants. It seems that the prevalence of long-COVID in individuals infected with the Omicron variant is the smallest, but current data are heterogeneous, and long-term data have, at this stage, an obviously shorter follow-up compared with the earlier variants. Fatigue is the most prevalent long-COVID symptom in all SARS-CoV-2 variants, but pain is likewise prevalent. The available data suggest that the infection with the Omicron variant results in fewer long-COVID symptoms compared to previous variants; however, the small number of studies and the lack of the control of cofounders, e.g., reinfections or vaccine status, in some studies limit the generality of the results. It appears that individuals infected with the historical variant are more likely to develop long-COVID symptomatology.

Antigenic escape is accelerated by the presence of immunocompromised hosts

The repeated emergence of SARS-CoV-2 escape mutants from host immunity has obstructed the containment of the current pandemic and poses a serious threat to humanity. Prolonged infection in immunocompromised patients has received increasing attention as a driver of immune escape, and accumulating evidence suggests that viral genomic diversity and emergence of immune-escape mutants are promoted in immunocompromised patients. However, because immunocompromised patients comprise a small proportion of the host population, whether they have a significant impact on antigenic evolution at the population level is unknown. We consider an evolutionary epidemiological model that combines antigenic evolution and epidemiological dynamics. Applying this model to a heterogeneous host population, we study the impact of immunocompromised hosts on the evolutionary dynamics of pathogen antigenic escape from host immunity. We derived analytical formulae of the speed of antigenic evolution in heterogeneous host populations and found that even a small number of immunocompromised hosts in the population significantly accelerates antigenic evolution. Our results demonstrate that immunocompromised hosts play a key role in viral adaptation at the population level and emphasize the importance of critical care and surveillance of immunocompromised hosts.

Genomic and structural mechanistic insight to reveal the differential infectivity of omicron and other variants of concern

BACKGROUND

The genome of SARS-CoV-2, is mutating rapidly and continuously challenging the management and preventive measures adopted and recommended by healthcare agencies. The spike protein is the main antigenic site that binds to the host receptor hACE-2 and is recognised by antibodies. Hence, the mutations in this site were analysed to assess their role in differential infectivity of lineages having these mutations, rendering the characterisation of these lineages as variants of concern (VOC) and variants of interest (VOI).

METHODS

In this work, we examined the genome sequence of SARS-CoV-2 VOCs and their phylogenetic relationships with the other PANGOLIN lineages. The mutational landscape of WHO characterized variants was determined and mutational diversity was compared amongst the different severity groups. We then computationally studied the structural impact of the mutations in receptor binding domain of the VOCs. The binding affinity was quantitatively determined by molecular dynamics simulations and free energy calculations.

RESULTS

The mutational frequency, as well as phylogenetic distance, was maximum in the case of omicron followed by the delta variant. The maximum binding affinity was for delta variant followed by the Omicron variant. The increased binding affinity of delta strain followed by omicron as compared to other variants and wild type advocates high transmissibility and quick spread of these two variants and high severity of delta variant.

CONCLUSION

This study delivers a foundation for discovering the improved binding knacks and structural features of SARS-CoV-2 variants to plan novel therapeutics and vaccine candidates against the virus.

Epidemiological and molecular description of nosocomial outbreak of COVID-19 Alpha (B.1.1.7) variant in Saudi Arabia

BACKGROUND

Nosocomial outbreaks frequently occurred during the Coronavirus disease 2019 (COVID-19) pandemic; however, sharing experiences on outbreak containment is vital to reduce the related burden in different locations.

OBJECTIVES

This article aims at sharing a practical experience on COVID-19 outbreak containment, including contact tracing, screening of target population, testing including molecular analysis, and preventive modalities. It also provides an epidemiological and molecular analysis of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‑CoV‑2) infection outbreak in a tertiary care hospital in Saudi Arabia.

METHODS

The outbreak occurred in a non-COVID medical ward at a tertiary care hospital in Jeddah, Saudi Arabia, from 22nd March and 15th April 2021. The multidisciplinary outbreak response team performed clinical and epidemiological investigations. Whole-Genome Sequencing (WGS) was implemented on selected isolates for further molecular characterization.

RESULTS

A total of eight nurses (20 % of the assigned ward nurses) and six patients (16.2 % of the ward admitted patients at the time of the outbreak) tested positive for the SARS-CoV-2 virus based on PCR testing. The outbreak investigation identified strong evidence of an epidemiologic link between the affected cases. WGS revealed a set of spike mutations and deletions specific to the Alpha variant (B.1.1.7 lineage). All the nurses had mild symptoms, and the fatality among the patients was 50 % (three out of the six patients).

CONCLUSIONS

The current nosocomial COVID-19 outbreak, caused by the Alpha variant, revealed multiple breaches in the adherence to the hospital infection control recommended measures. Containment strategies were successful in controlling the outbreak and limiting infection spread. Molecular analysis and genome sequencing are essential tools besides epidemiological investigation to inform appropriate actions, especially with emerging pathogens.

A Comprehensive Review on the Current Vaccines and Their Efficacies to Combat SARS-CoV-2 Variants

Since the first case of Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, SARS-CoV-2 infection has affected many individuals worldwide. Eventually, some highly infectious mutants-caused by frequent genetic recombination-have been reported for SARS-CoV-2 that can potentially escape from the immune responses and induce long-term immunity, linked with a high mortality rate. In addition, several reports stated that vaccines designed for the SARS-CoV-2 wild-type variant have mixed responses against the variants of concern (VOCs) and variants of interest (VOIs) in the human population. These results advocate the designing and development of a panvaccine with the potential to neutralize all the possible emerging variants of SARS-CoV-2. In this context, recent discoveries suggest the design of SARS-CoV-2 panvaccines using nanotechnology, siRNA, antibodies or CRISPR-Cas platforms. Thereof, the present comprehensive review summarizes the current vaccine design approaches against SARS-CoV-2 infection, the role of genetic mutations in the emergence of new viral variants, the efficacy of existing vaccines in limiting the infection of emerging SARS-CoV-2 variants, and efforts or challenges in designing SARS panvaccines.

Sensitivity to Vaccines, Therapeutic Antibodies, and Viral Entry Inhibitors and Advances To Counter the SARS-CoV-2 Omicron Variant

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) keeps evolving and mutating into newer variants over time, which gain higher transmissibility, disease severity, and spread in communities at a faster rate, resulting in multiple waves of surge in Coronavirus Disease 2019 (COVID-19) cases. A highly mutated and transmissible SARS-CoV-2 Omicron variant has recently emerged, driving the extremely high peak of infections in almost all continents at an unprecedented speed and scale. The Omicron variant evades the protection rendered by vaccine-induced antibodies and natural infection, as well as overpowers the antibody-based immunotherapies, raising the concerns of current effectiveness of available vaccines and monoclonal antibody-based therapies. This review outlines the most recent advancements in studying the virology and biology of the Omicron variant, highlighting its increased resistance to current antibody-based therapeutics and its immune escape against vaccines. However, the Omicron variant is highly sensitive to viral fusion inhibitors targeting the HR1 motif in the spike protein, enzyme inhibitors, involving the endosomal fusion pathway, and ACE2-based entry inhibitors. Omicron variant-associated infectivity and entry mechanisms of Omicron variant are essentially distinct from previous characterized variants. Innate sensing and immune evasion of SARS-CoV-2 and T cell immunity to the virus provide new perspectives of vaccine and drug development. These findings are important for understanding SARS-CoV-2 viral biology and advances in developing vaccines, antibody-based therapies, and more effective strategies to mitigate the transmission of the Omicron variant or the next SARS-CoV-2 variant of concern.

T cells in SARS-CoV-2 infection and vaccination

While antibodies garner the lion’s share of attention in SARS-CoV-2 immunity, cellular immunity (T cells) may be equally, if not more important, in controlling infection. Both CD8⁺ and CD4⁺ T cells are elicited earlier and are associated with milder disease, than antibodies, and T-cell activation appears to be necessary for control of infection. Variants of concern (VOCs) such as Omicron have escaped the neutralizing antibody responses after two mRNA vaccine doses, but T-cell immunity is largely intact. The breadth and patient-specific nature of the latter offers a formidable line of defense that can limit the severity of illness, and are likely to be responsible for most of the protection from natural infection or vaccination against VOCs which have evaded the antibody response. Comprehensive searches for T-cell epitopes, T-cell activation from infection and vaccination of specific patient groups, and elicitation of cellular immunity by various alternative vaccine modalities are here reviewed. Development of vaccines that specifically target T cells is called for, to meet the needs of patient groups for whom cellular immunity is weaker, such as the elderly and the immunosuppressed. While VOCs have not yet fully escaped T-cell immunity elicited by natural infection and vaccines, some early reports of partial escape suggest that future VOCs may achieve the dreaded result, dislodging a substantial proportion of cellular immunity, enough to cause a grave public health burden. A proactive, rather than reactive, solution which identifies and targets immutable sequences in SARS-CoV-2, not just those which are conserved, may be the only recourse humankind has to disarm these future VOCs before they disarm us.

Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7

New variants of SARS-CoV-2 are being reported worldwide. The World Health Organization has reported Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529) as the variants of concern. There are speculations that the variants might evade the host immune responses induced by currently available vaccines and develop resistance to drugs under consideration. The first step of viral infection in COVID-19 occurs through the interaction of the spike protein's receptor-binding domain (RBD) with the peptidase domain of the human ACE-2 (hACE-2) receptor. This study aims to get a molecular-level understanding of the mechanism behind the increased infection rate in the alpha variant. We have computationally studied the spike protein interaction in both the wild-type and B.1.1.7 variant with the hACE-2 receptor using molecular dynamics and MM-GBSA based binding free energy calculations. The binding free energy difference shows that the mutant variant of the spike protein has increased binding affinity for the hACE-2 receptor (i.e. ΔG(N501Y,A570D) is in the range -7.2 to -7.6 kcal mol^-1) and the results were validated using Density functional theory. We demonstrate that with the use of state-of-the-art computational approaches, we can, in advance, predict the virulent nature of variants of SARS-CoV-2 and alert the world healthcare system.

Structural bioinformatics analysis of SARS-CoV-2 variants reveals higher hACE2 receptor binding affinity for Omicron B.1.1.529 spike RBD compared to wild type reference

To date, more than 263 million people have been infected with SARS-CoV-2 during the COVID-19 pandemic. In many countries, the global spread occurred in multiple pandemic waves characterized by the emergence of new SARS-CoV-2 variants. Here we report a sequence and structural-bioinformatics analysis to estimate the effects of amino acid substitutions on the affinity of the SARS-CoV-2 spike receptor binding domain (RBD) to the human receptor hACE2. This is done through qualitative electrostatics and hydrophobicity analysis as well as molecular dynamics simulations used to develop a high-precision empirical scoring function (ESF) closely related to the linear interaction energy method and calibrated on a large set of experimental binding energies. For the latest variant of concern (VOC), B.1.1.529 Omicron, our Halo difference point cloud studies reveal the largest impact on the RBD binding interface compared to all other VOC. Moreover, according to our ESF model, Omicron achieves a much higher ACE2 binding affinity than the wild type and, in particular, the highest among all VOCs except Alpha and thus requires special attention and monitoring.

A Glycosylated RBD Protein Induces Enhanced Neutralizing Antibodies against Omicron and Other Variants with Improved Protection against SARS-CoV-2 Infection

SARS-CoV-2 has mutated frequently since its first emergence in 2019. Numerous variants, including the currently emerging Omicron variant, have demonstrated high transmissibility or increased disease severity, posing serious threats to global public health. This study describes the identification of an immunodominant non-neutralizing epitope on SARS-CoV-2 receptor-binding domain (RBD). A subunit vaccine against this mutant RBD, constructed by masking this epitope with a glycan probe, did not significantly affect RBD’s receptor-binding affinity or antibody-binding affinity, or its ability to induce antibody production. However, this vaccine enhanced the neutralizing activity of this RBD and its protective efficacy in immunized mice. Specifically, this vaccine elicited significantly higher-titer neutralizing antibodies than the prototypic RBD protein against Alpha (B.1.1.7 lineage), Beta (B.1.351 lineage), Gamma (P.1 lineage), and Epsilon (B.1.427 or B.1.429 lineage) variant pseudoviruses containing single or combined mutations in the spike (S) protein, albeit the neutralizing antibody titers against some variants were slightly lower than against original SARS-CoV-2. This vaccine also significantly improved the neutralizing activity of the prototypic RBD against pseudotyped and authentic Delta (B.1.617.2 lineage) and Omicron (B.1.1.529 lineage) variants, although the neutralizing antibody titers were lower than against original SARS-CoV-2. In contrast to the prototypic RBD, the mutant RBD completely protected human ACE2 (hACE2)-transgenic mice from lethal challenge with a prototype SARS-CoV-2 strain and a Delta variant without weight loss. Overall, these findings indicate that this RBD vaccine has broad-spectrum activity against multiple SARS-CoV-2 variants, as well as the potential to be effective and have improved efficacy against Omicron and other pandemic variants.

IMPORTANCE Several SARS-CoV-2 variants have shown increased transmissibility, calling for a need to develop effective vaccines with broadly neutralizing activity against multiple variants. This study identified a non-neutralizing epitope on the receptor-binding domain (RBD) of SARS-CoV-2 spike protein, and further shielded it with a glycan probe. A subunit vaccine based on this mutant RBD significantly enhanced the ability of prototypic RBD against multiple SARS-CoV-2 variants, including the Delta and Omicron strains, although the neutralizing antibody titers against some of these variants were lower than those against original SARS-CoV-2. This mutant vaccine also enhanced the protective efficacy of the prototypic RBD vaccine against SARS-CoV-2 infection in immunized animals. In conclusion, this study identified an engineered RBD vaccine against Omicron and other SARS-CoV-2 variants that induced stronger neutralizing antibodies and protection than the original RBD vaccine. It also highlights the need to improve the effectiveness of current COVID-19 vaccines to prevent pandemic SARS-CoV-2 variants.

Prevalence of Musculoskeletal Post-COVID Pain in Hospitalized COVID-19 Survivors Depending on Infection with the Historical, Alpha or Delta SARS-CoV-2 Variant

We compared the prevalence of musculoskeletal post-COVID pain between previously hospitalized COVID-19 survivors infected with the historical, Alpha or Delta SARS-CoV-2 variant. Data about musculoskeletal post-COVID pain were systematically collected through a telephone interview involving 201 patients who had survived the historical variant, 211 who had survived the Alpha variant and 202 who had survived the Delta variant six months after hospital discharge. Participants were recruited from non-vaccinated individuals hospitalized due to SARS-CoV-2 infection in one hospital of Madrid (Spain) during three different waves of the pandemic (historical, Alpha or Delta variant). Hospitalization and clinical data were collected from hospital medical records. In addition, anxiety/depressive levels and sleep quality were also assessed. The prevalence of musculoskeletal post-COVID pain was higher (p = 0.003) in patients infected with the historical variant (47.7%) than in those infected with the Alpha (38.3%) or Delta (41%) variants. A significantly (p = 0.002) higher proportion of individuals infected with the historical variant reported generalized pain (20.5%) when compared with those infected with the other variants. The prevalence of new-onset post-COVID musculoskeletal pain reached 80.1%, 75.2% and 79.5% of patients infected with the historical, Alpha or Delta variants, respectively. No specific risk factors for developing post-COVID pain were identified depending on the SARS-CoV-2 variant. In conclusion, this study found that musculoskeletal post-COVID pain is highly prevalent in COVID-19 survivors six months after hospital discharge, with the highest prevalence and most generalized pain symptoms in individuals infected with the historical variant. Approximately 50% developed “de novo” post-COVID musculoskeletal pain symptoms.

SARS-CoV-2 Nucleocapsid Protein Has DNA-Melting and Strand-Annealing Activities With Different Properties From SARS-CoV-2 Nsp13

Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the world and has had a devastating impact on health and economy. The biochemical characterization of SARS-CoV-2 proteins is important for drug design and development. In this study, we discovered that the SARS-CoV-2 nucleocapsid protein can melt double-stranded DNA (dsDNA) in the 5′-3′ direction, similar to SARS-CoV-2 nonstructural protein 13. However, the unwinding activity of SARS-CoV-2 nucleocapsid protein was found to be more than 22 times weaker than that of SARS-CoV-2 nonstructural protein 13, and the melting process was independent of nucleoside triphosphates and Mg²⁺. Interestingly, at low concentrations, the SARS-CoV-2 nucleocapsid protein exhibited a stronger annealing activity than SARS-CoV-2 nonstructural protein 13; however, at high concentrations, it promoted the melting of dsDNA. These findings have deepened our understanding of the SARS-CoV-2 nucleocapsid protein and will help provide novel insights into antiviral drug development.