An opinion on Wastewater-Based Epidemiological Monitoring (WBEM) with Clinical Diagnostic Test (CDT) for detecting high-prevalence areas of community COVID-19 Infections.

Wastewater-Based Epidemiological Monitoring (WBEM) is an efficient surveillance tool during the COVID-19 pandemic as it meets all requirements of a complete monitoring system including early warning, tracking the current trend, prevalence of the disease, detection of genetic diversity as well asthe up-surging SARS-CoV-2 new variants with mutations from the wastewater samples. Subsequently, Clinical Diagnostic Test is widely acknowledged as the global gold standard method for disease monitoring, despite several drawbacks such as high diagnosis cost, reporting bias, and the difficulty of tracking asymptomatic patients (silent spreaders of the COVID-19 infection who manifest nosymptoms of the disease). In this current reviewand opinion-based study, we first propose a combined approach) for detecting COVID-19 infection in communities using wastewater and clinical sample testing, which may be feasible and effective as an emerging public health tool for the long-term nationwide surveillance system. The viral concentrations in wastewater samples can be used as indicatorsto monitor ongoing SARS-CoV-2 trends, predict asymptomatic carriers, and detect COVID-19 hotspot areas, while clinical sampleshelp in detecting mostlysymptomaticindividuals for isolating positive cases in communities and validate WBEM protocol for mass vaccination including booster doses for COVID-19.

Animal Models to Test SARS-CoV-2 Vaccines: Which Ones Are in Use and Future Expectations.

Since late 2019 and early 2020, with the emergence of the COVID-19 pandemic, scientists are rushing to develop treatment and prevention methods to combat SARS-CoV-2. Among these are vaccines. In view of this, the use of animals as experimental models, both to investigate the immunopathology of the disease and to evaluate the efficacy and safety of vaccines, is mandatory. This work aims to describe, through recent scientific articles found in reliable databases, the animal models used for the in vivo testing of COVID-19 vaccines, demonstrating some possibilities of more advantageous/gold-standard models for SARS-CoV-2 vaccines. The majority of the studies use rodents and primates. Meanwhile, the most adequate model to be used as the gold standard for in vivo tests of COVID-19 vaccines is not yet conclusive. Promising options are being discussed as new tests are being carried out and new SARS-CoV-2 variants are emerging.

Comprehensive assessment of SARS-CoV-2 antibodies against various antigenic epitopes after naive COVID-19 infection and vaccination (BNT162b2 or ChAdOx1 nCoV-19).

Comprehensive assessment of SARS-CoV-2 antibodies against antigenic epitopes and cross-neutralization on variants is essential to monitor after infection or vaccination. From 32 COVID-19 patients and 40 vaccinated individuals [20 Oxford-AstraZeneca (AZ) and 20 Pfizer-BioNTech (BNT)], 348 serial sera are collected until 40 days after infection and 3 months after homologous booster vaccination. Antibody levels were monitored using a multiplex-bead assay including variant spike antigens, Roche (S1/RBD total) and a surrogate virus neutralization test (GenScript). Anti-S/S1/RBD levels were higher than anti-S2/N levels from 2 weeks after infection and were higher in severe infection (P < 0.05). Vaccination showed highest antibody levels after 1-month booster and had consistently high levels in the order of anti-full S, anti-RBD, anti-S1 and anti-S2. Infection induced higher anti-S2/N levels than prime vaccination (P < 0.05). Three months after BNT/BNT vaccination, antibody levels against S1/RBD and 23 variant antigens were higher than post-infection or AZ groups (P < 0.05). Regarding intraindividual changes from post-prime to post-boost vaccination, boost induced a 1.1- to 3.9-fold increase on multiplex-bead assay, 22.8- to 24.2-fold on Roche assay and 22.8- to 24.2-fold on GenScript assay. Post-prime levels by multiplex-bead assay predicted post-boost levels, but Roche and GenScript results were not predictive in the AZ group. The kinetics of SARS-CoV-2 antibody levels vary depending on the antigenic epitopes, assay kit, disease severity or vaccine type. Assessing seroconversion using multiplex-bead assays may contribute to monitoring the disease course, adjusting vaccination strategies, and accelerating vaccination efficacy.

COVID-19: Vaccines and therapeutics.

Coronavirus disease 2019 (COVID-19) is a communicable disease triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged as leading cause of death from a single infectious agent globally. Despite of rigorous protective measures, availability of multiple vaccines and with few approved therapeutics, the virus effect on the humankind throughout the world is perennial. COVID-19 has become the most urgent health concern with emergence of new challenging variants which outnumbered all other health issues and ensued in overwhelming number of reported deaths. In this unprecedented period of COVID-19 pandemic, scientists work round the clock for rapid development of efficient vaccines for prevention of infection and effective therapeutics for treatment. Here, we report the status of COVID-19 and highlight the ongoing research and development of vaccines and therapeutic strategies. It is necessary to know the present situation and available options to fight against the COVID-19 pandemic.

Emergence of New SARS-CoV2 Omicron Variants after the Change of Surveillance and Control Strategy.

In January 2022, there was a global and rapid surge of the Omicron variant of SARS-CoV-2 related to more transmission. This coincided with an increase in the incidence in Asturias, a region where rapid diagnosis and containment measures had limited the circulation of variants. METHODS: From January to June 2022, 34,591 variants were determined by the SNP method. From them, 445 were characterized by the WGS method and classified following pangolin program and phylogenic analysis. RESULTS: The Omicron variant went from being detected in 2438 (78%) samples in the first week of January 2021 to 4074 (98%) in the third week, according to the SNP method. Using the WGS method, 159 BA.1 (35.7%), 256 BA.2 (57.6%), 1 BA.4 (0.2%) and 10 BA.5 (2.2%) Omicron variants were found. Phylogenetic analysis detected that three new sub-clades, BA.2,3.5, BA.2.56 and BF1, were circulating. CONCLUSIONS: The increase in the incidence of SARS-CoV2 caused the circulation of new emerging variants. Viral evolution calls for continuous genomic surveillance.

SARS-CoV-2 Delta Variant is Recognized Through GRP78 Host-Cell Surface Receptor, In Silico Perspective.

Different SARS-CoV-2 new variants emerged and spread during the past few months, sparking infections and death counts. The new variant B.1.617 (delta variant) sparked in India in the past few months, causing the highest records. The B.1.617 variant of SARS-CoV-2 has the double mutations E484Q and L452R on its spike Receptor Binding Domain (RBD). The first mutation is like the reported South African and the Brazilian variants (501.V2 and B.1.1.248). This mutation lies in the region C480-C488, which we predicted before to be recognized by the host-cell receptor; Glucose Regulated Protein 78 (GRP78). In the current study, we test the binding affinity of the host-cell receptor GRP78 to the delta variant spike RBD using molecular docking and molecular dynamics simulations of up to 100 ns. Additionally, the ACE2-RBD is tested by protein-protein docking. The results reveal equal average binding affinities of the GRP78 against wildtype and delta variant spikes. This supports our previous predictions of the contribution of GRP78 in SARS-CoV-2 spike recognition as an auxiliary route for entry.

Effects of vaccination, new SARS-CoV-2 variants and reinfections on post-COVID-19 complications.

Post-COVID-19 complications involve a variety of long-lasting health complications emerging in various body systems. Since the prevalence of post-COVID-19 complications ranges from 8-47% in COVID-19 survivors, it represents a formidable challenge to COVID-19 survivors and the health care system. Post-COVID-19 complications have already been studied in the connection to risk factors linked to their higher probability of occurrence and higher severity, potential mechanisms underlying the pathogenesis of post-COVID-19 complications, and their functional and structural correlates. Vaccination status has been recently revealed to represent efficient prevention from long-term and severe post-COVID-19 complications. However, the exact mechanisms responsible for vaccine-induced protection against severe and long-lasting post-COVID-19 complications remain elusive. Also, to the best of our knowledge, the effects of new SARS-CoV-2 variants and SARS-CoV-2 reinfections on post-COVID-19 complications and their underlying pathogenesis remain to be investigated. This hypothesis article will be dedicated to the potential effects of vaccination status, SARS-CoV-2 reinfections, and new SARS-CoV-2 variants on post-COVID-19 complications and their underlying mechanisms Also, potential prevention strategies against post-COVID complications will be discussed.

Third Wave of the COVID-19 Pandemic: Prominence of Initial Public Health Interference.

Since the first news of a coronavirus-related pneumonia outbreak in December 2019, the virus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which causes COVID-19, has spread worldwide, with more than 100 million people infected in over 210 countries and two million deaths. In the UK (B.1.1.7), South Africa (B.1.351), Brazil (P.1), and India (B.1.617), independent SARS-CoV-2 lineages have recently been established. The virus accesses these variants via the angiotensin- converting enzyme-2 (ACE2) receptor due to several mutations in the immune-dominant spike protein. SARS-CoV-2 has caused substantial morbidity and mortality, as well as significant strain on public health systems and the global economy, due to the severity and intensity at which it has spread. COVID-19 vaccines have shown to be highly successful in clinical trials and can be used to fight the pandemic. The COVID-19 pandemic's environmental trends change at breakneck speed, making predictions based on traditional epidemiological knowledge particularly speculative. Following the first outbreak, the second wave of COVID-19 swept across the globe, infecting various countries. The third wave of coronavirus infection has already been experienced in a few countries. Many of us have said, "When this is over," but what exactly does that mean? Since the virus's first-, second-, and third-order effects manifest over various time periods, the pandemic will not be considered 'over' until the 'third phase' of the COVID-19 pandemic has passed. It is the best time to take preventative steps and immunize ourselves with vaccines in order to prepare for the predicted third wave of COVID-19 in some countries. In order to effectively suppress and monitor the COVID-19 pandemic, early and timely measures with improved social distancing policies should be enforced. We must continue critical public health efforts to suppress transmission and reduce mortality while working toward the rollout of a safe and efficient vaccine, and we must have the patience to listen, learn, improve, innovate, and evolve.

A New Wave of COVID-19 in 2021 with Unique Genetic Characters - Present Global Scenario and Beholding Onwards.

After the first report of a coronavirus-associated pneumonia outbreak in December 2019, the virus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) that causes the infection/disease (COVID-19) has developed into a pandemic, with >100 million people infected in over 210 countries along with two million people deceased from COVID-19 till today. Coronaviruses are positivestranded RNA viruses having restricted RNA polymerase proofreading ability thus it is very genetically susceptible to mutation. The evolution of SARS-CoV-2 from a single-point zoonotic introduction in Wuhan in November or December 2019 was widely expected, and viral sequence surveillance was developed as a result. When the first sequence of SARS-CoV-2 was released, a race to develop vaccines started, and several vaccines are now used worldwide. Independent SARS-CoV-2 lineages have recently been identified in the UK (B.1.1.7), Brazil (P.1), South Africa (B.1.351), and India (B.1.617). The recent appearance of several SARS-CoV-2 variant strains has shattered faith in the modern generation of vaccines' ability to provide enduring defense against infection. The risk of escaping natural and induced immunity has encouraged an urgency to comprehend the implications of these improvements, as well as a drive to develop new approaches to combat SARS-CoV-2 variants.

Whole-genome sequencing of SARS-COV-2 showed wide spread of B.1.525 in February 2021 in Libya.

Alpha (B.1.1.7) SARS-COV-2 variant was detected in September 2020 in minks and humans in Denmark and UK. This variant has several mutations in the spike region (S) which could increase the transmissibility of the virus 43-90% over previously circulating variants. The National Center for Disease Control (NCDC) announced on 24 February 2021 a 25% frequency of B.1.1.7 strain in Libya using a reverse-transcriptase quantitative PCR assay. This assay relies on the specific identification of the H69-V70 deletion in S gene which causes its failure of amplification (SGTF). This deletion is not specific for B.1.1.7, but is also characteristic of two other SARS-COV-2 variants. This study aimed to estimate the frequency of B.1.1.7 and identify other variants circulating in Libya in February 2021. We performed whole genome sequencing of 67 positive SARS-COV-2 samples collected on 25 February 2021 in Libya which were also tested by RT-qPCR for SGTF. Our results showed that 55% of samples had mutations specific to B.1.525 strain and only ~3% of samples belonged to B.1.1.7. These findings suggested that B.1.525 was spreading widely in Libya. The use of such RT-qPCR assay, although useful to track some variants, cannot discriminate between variants with H69-V70 deletion. RT-qPCR assays could be multiplexed to identify multiple variants and screen samples prior to sequencing. We emphasize on the need for providing whole-genome sequencing to the main COVID-19 diagnostic laboratories in Libya as well as establishing international collaboration for building capacity and advancing research in this time of the pandemic.

Cytidine deamination-induced perpetual immunity to SAR-CoV-2 infection is a potential new therapeutic target.

As the world is racing to develop perpetual immunity to the SARS-CoV-2 virus. The emergence of new viral strains, together with vaccination and reinfections, are all contributing to a long-term immunity against the deadly virus that has taken over the world since its introduction to humans in late December 2019. The discovery that more than 95 percent of people who recovered from COVID-19 had long-lasting immunity and that asymptomatic people have a different immune response to SARS-CoV-2 than symptomatic people has shifted attention to how our immune system initiates such diverse responses. These findings have provided reason to believe that SARS-CoV-2 days are numbered. Hundreds of research papers have been published on the causes of long-lasting immune responses and variations in the numbers of different immune cell types in COVID 19 survivors, but the main reason of these differences has still not been adequately identified. In this article, we focus on the activation-induced cytidine deaminase (AID), which initiates molecular processes that allow our immune system to generate antibodies against SARS-CoV-2. To establish lasting immunity to SARS-CoV-2, we suggest that AID could be the key to unlocking it.

Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity.

Glucose-regulated protein 78 (GRP78) might be a receptor for SARS-CoV-2 to bind and enter the host cell. Recently reported mutations in the spike glycoprotein unique to the receptor-binding domain (RBD) of different variants might increase the binding and pathogenesis. However, it is still not known how these mutations affect the binding of RBD to GRP78. The current study provides a structural basis for the binding of GRP78 to the different variants, i.e., B.1.1.7, B.1.351, B.1.617, and P.1 (spike RBD), of SARS-CoV-2 using a biomolecular simulation approach. Docking results showed that the new variants bound stronger than the wild-type, which was further confirmed through the free energy calculation results. All-atom simulation confirmed structural stability, which was consistent with previous results by following the global stability trend. We concluded that the increased binding affinity of the B.1.1.7, B.1.351, and P.1 variants was due to a variation in the bonding network that helped the virus induce a higher infectivity and disease severity. Consequently, we reported that the aforementioned new variants use GRP78 as an alternate receptor to enhance their seriousness.

Recent advances in SARS-CoV-2 Spike protein and RBD mutations comparison between new variants Alpha (B.1.1.7, United Kingdom), Beta (B.1.351, South Africa), Gamma (P.1, Brazil) and Delta (B.1.617.2, India).

New variants of SARS-CoV-2 Alpha (B.1.1.7); Beta (B.1.351) Gamma (P.1) and Delta (B.1.617.2) quickly spread in the UK, South Africa, Brazil and India, respectively. To address whether mutations in SARS-CoV-2 RBD spike protein could affect virus infectivity, peptides containing RBD amino acids mutations have been constructed and interacted with human ACE2 by computational methods. Our results suggest that mutations in RBD amino acids K417, E484, L452, T478 and N501 are expressively increasing the affinity of this protein with human angiotensin-converting enzyme 2 (ACE2), consequently, variants Alpha (B.1.1.7), Beta (B1.351), Gamma (P.1) and Delta (B.1.617.2) could be more infective in human cells compared with SARS-CoV-2 isolated in Wuhan-2019 and the Gamma and Delta variants could be the most infective among them.

SAR-CoV-2 infection, emerging new variants and the role of activation induced cytidine deaminase (AID) in lasting immunity.

As the world faces a fourth COVID-19 spike, scientists are learning a lot more about the new SARS-CoV-2 strains that were previously unknown. Currently, the Delta versions of SARS-CoV-2 have become the prevalent strains in much of the world since it first appeared in India in late 2020. Researchers believe they have discovered why Delta has been so successful: those infected with it create significantly more virus than those infected with the original strain of SARS-CoV-2, making it extremely contagious. This has redirected the focus to how our immune system defends us from these various pathogens and initiates such varied responses. Hundreds of research papers have been published on the origins of long-lasting immune responses and disparities in the numbers of different immune cell types in COVID 19 survivors, but the primary architect of these discrepancies has yet to be discovered. In this essay, we will concentrate on the primary architect protein, activation induced cytidine deaminase (AID), which triggers molecular processes that allow our immune system to produce powerful antibodies and SARS-CoV-2 specific B cells, allowing us to outwit the virus. We believe that if we ever achieve permanent immunity to SARS-CoV-2 infection, AID will be the key to releasing it.

SARS-CoV-2 new variants: Characteristic features and impact on the efficacy of different vaccines.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its new variants reported in different countries have posed a serious threat to human health and social fabrics worldwide. In addition, these new variants hindered the efforts of vaccines and other therapeutic developments. In this review article, we explained the emergence of new variants of SARS-CoV-2, their transmission risk, mortality rate, and, more importantly, the impact of each new variant on the efficacy of the developed vaccines reported in different literature and findings. The literature reported that with the emergence of new variants, the efficacy of different vaccines is declined, hospitalization and the risk of reinfection is increased. The reports concluded that the emergence of a variant that entirely evades the immune response triggered by the vaccine is improbable. The emergence of new variants and reports of re-infections are creating a more distressing situation and therefore demands further investigation to formulate an effective therapeutic strategy.

The Impact of Vaccination Worldwide on SARS-CoV-2 Infection: A Review on Vaccine Mechanisms, Results of Clinical Trials, Vaccinal Coverage and Interactions with Novel Variants.

BACKGROUND: The COVID-19 pandemic demanded a global effort towards quickly developing safe and effective vaccines against SARS-CoV-2. OBJECTIVE: This review aimed to discuss the main vaccines available, their mechanisms of action, results of clinical trials, and epidemiological behavior. The implications of viral variants were also debated. METHODS: A non-systematic literature review was performed between February and March 2021 by searching the Pubmed, Scopus, and SciELO databases, using different combinations of the following terms: "vaccines", "clinical trials" , "SARS-CoV-2", "Coronavirus", "COVID-19", "mechanisms of action". Data regarding clinical trials of SARS-CoV-2 vaccines and epidemiological information were also searched. RESULTS: The mechanisms of action included vector-virus, mRNA and inactivated virus vaccines. The vaccines showed positive results in phases 2/3 clinical trials. The efficacy of the mRNA 1273 and of mRNA BNT 162b2 vaccines were 94.1% and 95%, respectively. The effectiveness of the ChAdOx1 nCoV-19 vaccine varied according to the scheme, with an overall value of 70.4%. The Gam-COVID-Vac vaccine had an efficacy of 91.6%. Regarding the Ad26.COV2.S vaccine, 99% or more of seroconversion was observed in all subgroups 29 days after vaccination. The CoronaVac vaccine induced an immune response in 92% of the volunteers receiving 3ug and in 98% with 6ug, in comparison to 3% in the placebo group. CONCLUSION: Global efforts have resulted in vaccines being available in record time, with good safety and immunogenicity profile. However, only long-term studies can provide more information on the duration of immunity and the need for additional doses.

COVID-19 in Pregnancy-Perinatal Outcomes and Vertical Transmission Preventative Strategies, When Considering More Transmissible SARS-CoV-2 Variants.

The COVID-19 pandemic affected the physical and mental health of people around the world and left unprepared health care systems struggling to mount an adequate response. Understanding the impact of COVID-19 on pregnancy in terms of perinatal and fetal outcomes is essential to propose strategies for mminimising viral transmission. Overall, 91 pregnant women in labour, or with indication for induction of labour, with COVID-19 were admitted to hospital. On the day of admission, each pregnant woman underwent a nasopharyngeal swab to validate SARS-CoV-2 infection. Whenever delivery was by caesarean section, an amniotic fluid sample was collected after uterus incision. Neonates were tested twice: first by nasopharyngeal swab at birth and secondly either at 24 h after (when babies were isolated) or at discharge (when rooming-in). All samples underwent rRT-PCR testing for SARS-CoV-2. The SARS-CoV-2 RNA tests by nasopharyngeal swab of the pregnant women produced positive results in 47 patients. This cohort gave birth to 48 infants who were double tested by nasopharyngeal swab and included in the prospective observational study. Moreover, in this same cohort, 39 amniotic fluid samples were taken during caesarean section. All samples underwent rRT-PCR testing for SARS-CoV-2 and came back negative. The study results suggest a low risk of vertical transmission of COVID-19 and favourable perinatal outcomes due to adequate preventative strategies. This approach may prove to be more beneficial in the new SARS-CoV-2 variants era.

Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data.

The evolution of the SARS-CoV-2 new variants reported to be 70% more contagious than the earlier one is now spreading fast worldwide. There is an instant need to discover how the new variants interact with the host receptor (ACE2). Among the reported mutations in the Spike glycoprotein of the new variants, three are specific to the receptor-binding domain (RBD) and required insightful scrutiny for new therapeutic options. These structural evolutions in the RBD domain may impart a critical role to the unique pathogenicity of the SARS-CoV-2 new variants. Herein, using structural and biophysical approaches, we explored that the specific mutations in the UK (N501Y), South African (K417N-E484K-N501Y), Brazilian (K417T-E484K-N501Y), and hypothetical (N501Y-E484K) variants alter the binding affinity, create new inter-protein contacts and changes the internal structural dynamics thereby increases the binding and eventually the infectivity. Our investigation highlighted that the South African (K417N-E484K-N501Y), Brazilian (K417T-E484K-N501Y) variants are more lethal than the UK variant (N501Y). The behavior of the wild type and N501Y is comparable. Free energy calculations further confirmed that increased binding of the spike RBD to the ACE2 is mainly due to the electrostatic contribution. Further, we find that the unusual virulence of this virus is potentially the consequence of Darwinian selection-driven epistasis in protein evolution. The triple mutants (South African and Brazilian) may pose a serious threat to the efficacy of the already developed vaccine. Our analysis would help to understand the binding and structural dynamics of the new mutations in the RBD domain of the Spike protein and demand further investigation in in vitro and in vivo models to design potential therapeutics against the new variants.