SARS

Wastewater samples are showing signs of sustained higher levels of SARS-CoV-2 in Gauteng, KwaZulu-Natal, the Free State and the Western Cape.

The work of the NICD and the Saccess teams is acknowledged. To support the sector, the initiative partners are happy to announce the launch by the NICD of an online dashboard to communicate wastewater results to stakeholders, including the public and policy-makers. The main aim of the programme is to share knowledge, stimulate research and innovation on water quality, sanitation and health in support of the government’s initiatives aimed at managing and curbing the spread of SARS-CoV-2. The programme consists of planned, interrelated activities aimed at achieving the objectives, by producing specified outputs. The Water Research Commission (WRC) continues to lead and fund this national initiative in partnership with the South African Local Government Association (Salga), which is coordinated and managed by the National Institute for Communicable Diseases (NICD) through a network of laboratories and several partnerships. As we progress, we have added the component of genomics to keep monitoring variants and their changes. Wastewater-based surveillance deals with a remnant nucleic acid particle of the SARS-CoV-2 virus and not a live virus, which means the procedure is safe.

T cell responses were measured to three SARS-CoV-2-associated antigens, as well as the endemic coronaviruses HCoV-OC43 and HCoV-NL63.

The N peptide pool induced a CD4+ T cell response in 70.4% of previously infected patients after three months, 92.3% at six months, and 55.6% at nine months, equivalent to the spike and membrane proteins. Adding structural SARS-CoV-2 protein sequences to the spike glycoprotein could boost the efficacy of COVID-19 mRNA vaccines in the future. CD4+ T cells specific for the N-terminal (S-1) and C-terminal (S-2) spike glycoprotein peptide pools, as well as the membrane (M) and nucleocapsid (N) peptide pools, were found in higher numbers in previously infected people. The longevities of cellular and humoral responses of previously infected participants to SARS-CoV-2 were examined. Twenty-seven of the initial 36 infected patients were followed for nine months following initiation of symptoms. Study subjects who reacted to OC43-1 and NL63-1 had a greater percentage of S-1-specific T cells. Compared to the non-reactive group, NL63-2-reactive T cells revealed just a minor change. The S glycoproteins generated by SARS-CoV-2 and the endemic coronaviruses HCoV-OC43 and HCoV-NL63 were tested for cross-reactivity. However, T cells respond to extra structural proteins such as envelope (E), membrane (M), and nucleocapsid (N) in previously infected patients (N). A control group that had not been exposed was matched in age and gender. According to recent studies, neutralizing antibody titers fall dramatically throughout the first eight months after symptom onset and fall by up to 53% after a year. The current vaccines used against SARS-CoV-2 only target viral host cell entry mechanisms such as the spike (S) glycoprotein and the receptor-binding domain.

India News: BENGALURU: The Indian Institute of Science (IISc) on Monday said that a drug used to treat asthma and allergies can bind to and block a crucial ...

The exact mechanisms by which it works still need to be fully understood,” Hussain said. Montelukast, on the other hand, was found to bind strongly and stably to Nsp1, allowing the host cells to resume normal protein synthesis.” To analyse these and identify which drugs may work inside the cell was a challenge,” says Mohammad Afsar, former project scientist at MRDG, currently a postdoc at the University of Texas

A drug used to treat asthma and allergies can bind to and block a crucial protein produced by the virus SARS-CoV-2, and reduce viral replication in human ...

They found that the drug was able to reduce viral numbers in infected cells in the culture. “The anti-HIV drug (saquinavir) showed good affinity, but not good stability.” Montelukast, on the other hand, was found to bind strongly and stably to Nsp1, allowing the host cells to resume normal protein synthesis. In the study published in eLife, the researchers show that the drug binds strongly to one end (‘C-terminal’) of a SARS-CoV-2 protein called Nsp1, which is one of the first viral proteins unleashed inside the human cells.

Researchers at the IISc found that Montelukast, used to reduce inflammation caused by conditions like asthma, blocks SARS-CoV-2 from replicating.

Montelukast, on the other hand, was found to bind strongly and stably to Nsp1, allowing the host cells to resume normal protein synthesis," Tanweer Hussain, Assistant Professor in the Department of Molecular Reproduction said in a statement. The researchers screened over 1,600 US Food and Drug Administration (FDA)-approved drugs in order to find the ones that bound strongly to Nsp1 using computational modelling. This protein can bind to ribosomes the protein-making machinery inside our immune cells and shut down the synthesis of vital proteins required by the immune system, thereby weakening it.

Nonvaccination is expected to result in amplification of disease transmission in unvaccinated subpopulations, but the communicable nature of infectious diseases ...

Increased mixing between vaccinated and unvaccinated groups increased final epidemic size among vaccinated people; conversely, more like-with-like mixing decreased final epidemic size among vaccinated people but resulted in enhancement of the degree to which risk among vaccinated people could be attributed to unvaccinated people. Using simple mathematical modelling, we have shown that, although risk associated with avoiding vaccination during a virulent pandemic accrues chiefly to those who are unvaccinated, the choice of some individuals to refuse vaccination is likely to affect the health and safety of vaccinated people in a manner disproportionate to the fraction of unvaccinated people in the population. As like-with-like mixing increased, contribution to infection risk among vaccinated people was increasingly derived from (less and less common) interactions with unvaccinated people, increasing the value of ψ. We found similar patterns in sensitivity analyses in which vaccine coverage was increased from 80% to 99% ( Figure 3). Increasing population vaccination coverage decreased the attack rate among vaccinated people (as expected, owing to indirect protective effects) but further increased the relative contribution to risk in vaccinated people by those who were unvaccinated at any level of like-with-like mixing. However, we find that the degree to which people differentially interact with others who are like themselves is likely to have an important impact on disease dynamics and on risk in people who choose to get vaccinated. The value of ψ would increase above 1 either because of an increased fraction of infections derived from contact with unvaccinated people or a decrease in the amount of contact between the groups (i.e., an increase in like-with-like mixing). For example, with random mixing, peak incidence was simultaneous in the vaccinated and unvaccinated groups, but with strong like-with-like mixing the epidemic peak among vaccinated people occurred about 1 week later than among unvaccinated people; population-adjusted peak incidence was 4 times higher in the unvaccinated population than in the vaccinated population with random mixing, but about 30 times higher with strong like-with-like mixing ( Figure 1). For our model, with 20% of the population unvaccinated, when random mixing is assumed (η = 0), 20% of the contacts a vaccinated person has would be expected to occur with unvaccinated people. We calculated a quantity (ψ), which we defined as the fraction of all infections among vaccinated people that derived from contact with unvaccinated people, divided by the fraction of all contacts that occurred with unvaccinated people. We sought to contrast contribution to epidemic size and risk estimates by subpopulation, and to understand the impact of mixing between vaccinated and unvaccinated groups on expected disease dynamics. In our model, like-with-like mixing is determined by a constant (η), with random mixing occurring when η = 0, complete like-with-like mixing occurring when η = 1 and intermediate degrees of like-with-like mixing occurring at intermediate values. 13, 24, 25 To better understand the implications of the interplay between vaccinated and unvaccinated populations under different assumptions about population mixing, we constructed a simple susceptible–infectious–recovered model to reproduce the dynamics of interactions between vaccinated and unvaccinated subpopulations in a predominantly vaccinated population. The contact-adjusted contribution of unvaccinated people to infection risk was disproportionate, with unvaccinated people contributing to infections among those who were vaccinated at a rate higher than would have been expected based on contact numbers alone.

Vaccine-induced antibody responses to the original SARS-CoV-2 strain and the omicron and delta variants are lower in patients with non-Hodgkin lymphoma.

The researchers also observed a correlation between antibody responses and age. Patients with NHL who received anti-CD20-directed therapies within 1 year before their initial vaccination exhibited the greatest impairment in response to vaccination. Neutralizing antibody titers were 6-fold lower against delta and 42-fold lower against omicron. All healthy control individuals developed neutralizing antibodies, compared with 68% of the NHL patients. The study included 121 patients with NHL who received 2 doses of a COVID-19 vaccine. The team used the WA1/2020 strain of SARS-CoV-2, which closely resembles the original Wuhan strain.

A team of UK-based scientists has recently developed a within-host model to determine the dynamics of SARS-CoV-2 infection in the upper respiratory tract of ...

As estimated by the model, the infectiousness of individuals can persist for up to 8 days, whereas they can test positive in PCR test for up to 12 days. The current model revealed a within-host reproduction number of 11. The rate of production of infectious virus from infected cells was estimated to be 3.7 plaque-forming unit (PFU)/ml per day. It is known that the infectiousness of individuals is directly proportional to their viral load in the respiratory tract. The study was conducted on the participants of a human challenge study. Various epidemiological studies have indicated that the risk of SARS-CoV-2 infection in susceptible individuals depends on the rate of contact and probability of transmission.

Inflammation is one of the most serious consequences of infection and is a hallmark of severe SARS-CoV-2. Recent studies show that SARS-CoV-2 induces the ...

Both of these studies represent real progress in understanding the inflammation that occurs in patients with severe SARS-CoV-2 and reveals potential treatments against inflammation that could significantly reduce the danger of SARS-CoV-2 infection. By using an antibody treatment, researchers believed that the antibodies would block the interleukin-17 receptors so that the ORF8 protein could not bind to the receptors. To further investigate the relationship between ORF8 and the interleukin-17 receptors, Wu et al. examined the interactions between three common ORF8 variants and the interleukin-17 receptors. These results would indicate how well ORF8 could mimic the effects of interleukin-17 inside the cell. While this determined that ORF8 interacted with the interleukin-17 receptors, it was unclear whether ORF8 directly triggered inflammation or if it promoted inflammation by increasing the expression of interleukin-17. So, how effective could ORF8 be at actually mimicking the effects of interleukin-17? To test their hypothesis, the researchers examined three different SARS-CoV-2 proteins: NSP2, ORF7a, and ORF8, and tested their interactions with interleukin-17 receptors. To their surprise, only ORF8 exhibited interactions with the interleukin-17 receptors. Inflammation is one of the most serious consequences of viral infection and is a hallmark of severe SARS-CoV-2. When SARS-CoV-2 replication and inflammation are left unchecked, they not only lead to severe immediate consequences but long-term consequences. successfully demonstrated that the interactions between ORF8 and interleukin-17 receptors caused inflammation, but how could those interactions be prevented? Interleukin-17 is a family of proteins that are produced by T-helper immune cells.

These surveillance studies evaluating genetic changes of SARS-CoV-2 have been identified as critical by the CDC that can affect many aspects of public health including transmission, disease severity, diagnostics, therapeutics, and vaccines. Peer Review ...

Furthermore, we analyzed the genomic epidemiology and sequencing applications of SARS-CoV-2 for the CDC surveillance program between March 2021 and June 2021, with a focus on variant and lineage determination, quality of sequencing results between sequencing instruments and the association between Ct values, genome coverage and variant detection. Samples were selected for inclusion in the sequencing study based on a minimum threshold of SARS-CoV-2 detection by RT-PCR (N Gene Ct value threshold ≤ 30). Further investigation of the SARS-CoV-2 PCR data of the samples in this study reveals a direct correlation between the ability to detect SARS-COV-2 viral content by sequencing and the Ct values of the N gene. The prevalence and transmission of Delta (B.1.617) continued to rise and was the most prevalent between the months of July and December 2021 (Fig. 6a). The only CDC variant of interest that was not identified in our study within the sample set and time frame tested was B.1.617.3. Further details on trends in lineage discovery in our study as the data continued to be accumulated between the months of June 2021 to February 2022 demonstrated a rapid rise and major prevalence of the Omicron variant BA.1 are provided in Additional file 1: Table S1 and Fig. 6a and b. In summary, the CDC surveillance screening program for SARS-CoV-2 variant transmission using whole viral genome sequencing is an important approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic. We identified only eight samples in our dataset that had mean genome coverage less than 100×. Of the remaining 24,433 samples we determined that a mean Ct value of 26.5 for NextSeq 550 and 27.9 for NovaSeq 6000 was a threshold for producing high quality genome sequencing reads (Fig. 5a–c). We saw a clear difference in mean genome coverage among the four groups (Fig. 5). Group 1, with lowest Ct samples had the highest genomic coverage while group 4 with highest Ct values, had the lowest mean genomic coverage. The average sequencing coverage between the two was ascertained using average sequencing coverage over the SARS-COV-2 genome and fraction of nucleotides masked due to sequencing ambiguity in the consensus sequence generated. Of all the samples, 73.5% (17,974) samples were sequenced on the NextSeq 550, while 26.46% (6467) were sequenced on the NovaSeq 6000. The application created a cumulative metadata file containing the metadata associated with the samples transferred and transferred the file to the S3 bucket. Each sample was evaluated for the presence of the virus in the sequencing data using a k-mer based algorithm prior to performing variant calling steps. IBX was designated by the CDC to participate in its Genomic Surveillance for SARS-CoV-2 Variants program [ 1]. This program conducts genomic surveillance using a random sampling of previously confirmed positive samples from across the U.S., including all 50 states, Washington DC, Puerto Rico and major U.S. territories and possessions. Herein we present the initial results correlating RT-PCR quality control metrics with sample collection and sequencing methods from full SARS-CoV-2 viral genomic sequencing of 24,441 positive patient samples between April and June 2021.

Keep multisystem inflammatory syndrome (MIS) in mind even if patients think they haven't had COVID-19, say experts.

So, the immune response is probably not to the same amplitude.” Any patient that’s presenting with these kinds of symptoms, it should be considered whether or not they had a confirmed COVID diagnosis in the preceding month,” Dr Howard-Jones said. “The laboratory test results will be quite abnormal, particularly in terms of inflammation markers, like the C-reactive protein or the erythrocyte sedimentation rate. So those kinds of numbers are very reassuring, particularly when you consider the number of severe cases of COVID-19,” she highlighted. In the literature, there are definitely more case reports of MIS from COVID-19 infection, rather than the vaccine itself,” she explained. In both cases, the patients were young, with mostly mild or no underlying medical conditions when they were diagnosed with a SARS-CoV-2 infection.

Coronavirus disease 2019 (COVID-19) has been the world's greatest respiratory virus pandemic of this century, with over 505 million SARS-CoV-2 cases and 6.2 ...

After BNT162b2 dose 1, 99.65% of SARS-CoV-2 infection-naive subjects were seroconverted, and >99.9% were seroconverted following dose 2. After BNT162b2 vaccine doses 1 and 2, the post-vaccination period was limited to ≥3 weeks and ≥3 weeks, respectively. The management of COVID-19 necessitates a thorough understanding of immune responses to SARS-CoV-2 vaccinations.

In a recent study posted to the medRxiv* preprint server, researchers analyzed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outcomes by ...

Also, COVID-19 vaccines minimize the likelihood of severe SARS-CoV-2 outcomes in both cancer patients and non-cancer patients. Researchers discovered that cancer patients receiving chemotherapy were still linked to greater odds of severe COVID-19, 60-day all-cause death, and hospitalization even when excluding hematologic malignancies. The team used Firth-corrected, covariate-adjusted logistic regression to analyze the connection between cancer type, cancer status, and cancer therapy and four SARS-CoV-2 outcomes: COVID-linked hospital admission, intensive care unit (ICU) admission, death, and a cumulative "severe COVID-19" outcome that combines the first three. Regarding cancer types, lung cancer and hematologic malignancies were substantially linked to a greater risk of SARS-CoV-2-linked hospitalization. While hematologic malignancies were connected to COVID-19-associated ICU admission and death, breast cancer, prostate cancer, and melanoma were not linked to poor COVID-19 outcomes. Previous studies found that cancer patients have a higher risk of COVID-19-related death, yet it is unclear how this relationship differs by cancer site, cancer therapy, and SARS-CoV-2 vaccination status.

Researchers at the University of Texas Medical Branch recently confirmed the presence of neutralizing antibodies to SARS-CoV-2 in a common subcutaneous ...

Miller points out that patients and health care providers frequently inquire about the presence of SARS-CoV-2 antibodies in their immunoglobulin products. The presence of neutralizing antibodies has value for future immunoglobulin-based modalities and is of clear benefit to this patient population." Patients with immunodeficiency diseases are often treated with therapeutic immunoglobulin, an antibody therapy that provides those with weakened immune systems or other diseases the antibodies they need to fight off infections.

Hyperinflammation is responsible for much of the damage in acute Covid-19. Generalized inflammation is a major contributor to long Covid.

Genetic analysis of the cell cultures that triggered the cGAS–STING pathway revealed an increased induction of DNA damage responses (DDR) — an elaborate network of genes in charge of recognizing and tending to DNA damage. Instead of the spike protein-containing kidney cells they used for their initial co-cultures, the team directly infected a range of human endothelial cell lines with a vesicular stomatitis virus (VSV) that had been engineered to express the SARS-CoV-2 spike protein. More research needs to be done to understand the contribution of type 1 interferon to hyper-inflammation and severe Covid-19. turned to the microscope; they observed that spike protein-induced syncytia were peppered with ruptured nuclei and with micronuclei. To study the formation of syncytia and its knock-on effects, Liu et al. Curious to determine how exactly cell fusion triggers IFN-β activation, the team of scientists turned to one of the central signaling pathways of the innate immune system, the cGAS–STING pathway (Figure 3). This pathway kicks off with the detection of misplaced DNA by an enzyme called cGAMP synthase (cGAS). DNA is usually found in the nucleus of a cell, so its presence in the cytoplasm indicates either cellular damage or microbial infection. Only the unmutated spike protein induced the expression of IFN-β. They also found that cells overexpressing TMPRSS2 displayed higher levels of IFN-β expression. cGAS binds to the misplaced DNA, triggering the formation of cyclic GMP-AMP (cGAMP). This, in turn, goes on to bind to Stimulator of Interferon Genes ( STING), a protein in charge of inducing the production of type 1 interferons such as IFN-β. With STING in the game, interferon regulatory factor 3 (IFR3) undergoes phosphorylation. As expected, the researchers witnessed cell fusion between the spike protein-containing cells and the endothelial cells. Following cell fusion and the formation of syncytia, Liu et al. The presence of syncytia, along with alveolar destruction and massive blood clotting, are all characteristic of severe Covid-19. Syncytia are large, cell-like structures that form when two or more cells join together; essentially, an amorphous mass of cytoplasm and nuclei (Figure 1). Even though syncytia are crucial to the formation of our muscle tissue, when induced in response to viral infection they are pathological. Although the impacts of SARS-CoV-2 infection have been recorded across the board —from the liver to the heart to the brain, and beyond— nowhere is the damage quite as intense as in the lungs.

The CDC said that 75% of children under aged 17 and more than 60% of adults up to age 49 have evidence of prior infection with SARS-CoV-2, the virus that ...

Among adults aged 18 to 49 years, from 36.5% (95% CI, 35.7%-37.4%) to 63.7% (95% CI, 62.5%-64.8%) Among adults aged 50 to 64 years, 28.8% (95% CI, 27.9%-29.8%) to 49.8% (95% CI, 48.5%-51.3%) Among adolescents aged 12 to 17 years, from 45.6% (95% CI, 44.4%-46.9%) to 74.2% (95% CI, 72.8%-75.5%) Among those 65 years and older, from 19.1% (95% CI, 18.4%-19.8%) to 33.2% (95% CI, 32.2%-34.3%) Among children aged 0 to 11 years, from 44.2% (95% CI, 42.8%-45.8%) to 75.2% (95% CI , 73.6%-76.8%) Overall US seroprevalence increased from 33.5% (95% CI, 33.1%-34.0%) to 57.7% (95% CI, 57.1%-58.3%). Sera are tested for anti-nucleocapsid (anti-N) antibodies, which are produced in response to infection.

A recent paper posted to the bioRxiv* preprint server depicted the differential allosteric response of the severe acute respiratory syndrome coronavirus 2 ...

When the SARS-CoV-2 original variant S was compared to the four viral variants: Omicron BA.1, Delta plus, Delta, and Alpha, it was clear that the responses of the variants to LA removal varied dramatically. A strengthened allosteric linkage was observed between the FA site and the furin cleavage site in Delta plus, Omicron, and Delta compared to the original S, but the link to V622-L629 was weakened. In Omicron, the FA site had a weaker connection with the H146-E156, V622-L629, and S71-R78 regions, but the RBM, the furin cleavage site, and L249-G257 area demonstrated stronger binding to the FA site. In the present investigation, the researchers compared the response of the SARS-CoV-2 S variants to the removal of LA using hundreds of dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations. Except for the S71-R78 and RBM, the allosteric linkages in Alpha were quite identical to those in the original S protein. In their prior work, the present authors demonstrated that the FA site was allosterically coupled with the antigenic epitope or to functional motifs of SARS-CoV-2 for membrane fusion employing dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations.

The genome of SARS-CoV-2 has rapidly acquired numerous mutations, giving rise to several Variants of Concern (VOCs) with altered epidemiological, immunological, and pathogenic properties. Methods. As cell culture models are important tools to study viruses ...

Images were taken at all time points from 2 to 96 h p.i.. For 72, 80, and 96 h p.i., representative images of SARS-CoV-2 non-VOC, the five VOCs, and an uninfected control are shown to illustrate the difference in CPE development and progression between different virus strains. Consensus sequences of the viral lineages determined by WGS were submitted to the GISAID database ( www.gisaid.org) with the following accession numbers: non-VOC/B.1.1 passage 1 (EPI_ISL_10201350), passage 3 (EPI_ISL_10201358), passage 4 replicate I (EPI_ISL_10201359), passage 4 replicate II (EPI_ISL_10201360), passage 4 replicate III (EPI_ISL_10201362), Alpha/B.1.1.7 patient sample (EPI_ISL_1143971), passage 2 (EPI_ISL_10201372), passage 3 (EPI_ISL_10201380), passage 4 replicate I (EPI_ISL_10201369), passage 4 replicate II (EPI_ISL_10201370), passage 4 replicate III (EPI_ISL_10201371), Beta/B.1.351 patient sample (EPI_ISL_10201379), passage 4 (EPI_ISL_10201351), passage 5 replicate I (EPI_ISL_10201352), passage 5 replicate II (EPI_ISL_10201353), passage 5 replicate III (EPI_ISL_10201354), Gamma/P.1 patient sample (EPI_ISL_1349034), passage 2 (EPI_ISL_10201363), passage 3 (EPI_ISL_10201364), passage 4 replicate I (EPI_ISL_10201365), passage 4 replicate II (EPI_ISL_10201366), passage 4 replicate III (EPI_ISL_10201367), Delta/B.1.617.2 patient sample (EPI_ISL_2260430), passage 2 (EPI_ISL_10201368), passage 3 replicate I (EPI_ISL_10201377), passage 3 replicate II (EPI_ISL_10201375), passage 3 replicate III (EPI_ISL_10201376), and Omicron/B.1.1.529 patient sample (EPI_ISL_8379763), passage 1 (EPI_ISL_10201373), passage 2 (EPI_ISL_10201378), passage 3 replicate I (EPI_ISL_10201355), passage 3 replicate II (EPI_ISL_10201356), passage 3 replicate III (EPI_ISL_10201357). Images were taken at all time points from 2 to 96 h p.i.. For 72, 80, and 96 h p.i., representative images of SARS-CoV-2 non-VOC, the five VOCs, and an uninfected control are shown to illustrate the difference in CPE development and progression between different virus strains. Images were taken at all time points from 2 to 96 h p.i.. For 72, 80, and 96 h p.i., representative images of SARS-CoV-2 non-VOC, the five VOCs, and an uninfected control are shown to illustrate the difference in CPE development and progression between different virus strains. Cell lines were infected with the SARS-CoV-2 isolates non-VOC/B.1.1, Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, Delta/B.1.617.2, and Omicron/B.1.1.529 in triplicates (n = 3) at an MOI of 0.0001 in 4 mL of their respective cell culture media for 2 h. One of the most widely used cell lines for working with viruses in general is the African Green Monkey-derived Vero E6 kidney cell line [ 23, 24]. It was also the most commonly used cell line for isolating and propagating the newly emerging virus SARS-CoV-2 in late December 2019 and early 2020. In our experiments with Vero E6 infection, the time point of reaching the highest infectivity correlated well with the visual appearance of CPE for all SARS-CoV-2 variants. We show distinct differences in viral replication kinetics of the SARS-CoV-2 non-VOC and five VOCs on the three cell culture models Vero E6, Caco-2, and Calu-3. A standard curve for quantification of genome copy numbers was performed in parallel using purified SARS-CoV-2 viral RNA with genome copy numbers assessed by reverse transcriptase droplet digital PCR (RT-ddPCR) as previously described [ 37]. After verifying the integrity of the SARS-CoV-2 isolate in the cell culture supernatant by RT-qPCR utilizing the Xpert® Xpress SARS-CoV-2 (#XPRSARS-COV2-10, Cepheid, Sunnyvale, CA, USA), the isolates were further propagated on Vero E6 cells. All cells were maintained at 37 °C in a humidified atmosphere in the presence of 5% CO2. All cell lines were free of mycoplasma contaminations as tested by PCR. The authenticity of the used human cell lines was determined by SNP typing. The genome of SARS-CoV-2 has rapidly acquired numerous mutations, giving rise to several Variants of Concern (VOCs) with altered epidemiological, immunological, and pathogenic properties.

529) SARS-CoV-2 variant contains an unusually high number of mutations in the spike protein, raising concerns of escape from vaccines, convalescent serum and therapeutic drugs. Here we analyzed the degree to which Omicron pseudovirus evades neutralization ...

The primers for genotyping were 5′-CTTGGTGATATGTGGGGTAGA-3′ and 5′-CGCTTCATCTCCCACCACTT-3′ as shown previously (13). Male and female mice aged at four-week-old were anaesthetized and challenged with 1.0 × 103 PFU of SARS-CoV-2 Omicron (in 20μL) by the intranasal route (10μL per nostril). At 2 hours post inoculation, ACE2-Fc (3N39v2, 20mg/kg) was administered by intravenous injection. CAG-hACE2 transgenic mice (hACE2-Tg) were obtained from the Laboratory Animal Resource Bank of the National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN). These mice were maintained by crossing with wild type C57BL/6 mice. Pseudotyped reporter virus assays were conducted as previously described (5). With a plasmid encoding the SARS-CoV-2 spike protein (addgene #145032) as a template, mutations for variants of concern, including omicron BA.1 and BA.2, as well as the ΔC19 deletion (with 19 amino acids deleted from the C terminus) were cloned into pcDNA4TO (Invitrogen) ( 38). Pangolin CoV GD-1, Bat CoV RsSHC014, and WIV1 spike proteins were synthesized (Integrated DNA Technologies) and cloned into pcDNA4TO (Invitrogen) in the form of ΔC19 ( 10, 39). Pangolin CoV GX-P5L, Bat CoV RaTG13, and Rs4231 RBDs were synthesized (Integrated DNA Technologies) and cloned into the RBD of SARS-CoV-1 (ΔC19) ( 5, 10, 11, 39). Spike protein-expressing pseudoviruses with a luciferase reporter gene was prepared by transfecting plasmids (OmicronΔC19, psPAX2-IN/HiBiT ( 40), and pLenti firefly) into LentiX-293T cells with Lipofectamine 3000 (Invitrogen). After 48 hours, supernatants were harvested, filtered with a 0.45 μm low protein-binding filter (SFCA), and frozen at –80 °C. The 293T/ACE2 cells were seeded at 10,000 cells per well in 96-well plates. We collected peripheral blood from 12 individuals (7 males, 5 females, age 24 to 56, mean 37.5) at 3 months post vaccination with two doses of the Pfizer-BioNTech vaccine, BNT162b2. Peripheral blood was also collected from 11 SARS-CoV-2 convalescent individuals (7 males, 4 females, age 50 to 83, mean 69) before the Delta variant wave (December 2020 through January 2021), and 18 SARS-CoV-2 convalescent individuals (15 males, 3 females, age 36 to 77, mean 56.6) during or after the Delta wave (August 2021 through October 2021). The study size was determined by the number of samples that were available from the cohort study and not based on any power calculations. Amino acid mutation frequencies in the spike protein for each variant (Alpha = 1,138,704, Beta = 40,135, Gamma = 117,200, Delta = 3,441,137, and Omicron = 5,469 sequences) were extracted from the report of outbreak.info (https://outbreak.info/compare-lineages?pango=Delta&pango=Omicron&pango=Alpha&pango=Beta&pango=Gamma&gene=S&threshold=0.2&nthresh=1&sub=false&dark=true%29.%20Accessed%2017%20December%202021.) as of December 17, 2021. Furthermore, we found that the side chain of R493 could form a direct hydrogen bond with N31 of ACE2(3N39) instead of K35 (fig. S4E). Therefore, consistent with the results of the neutralization assay, engineered ACE2 is expected to have no or little loss of affinity for the RBD of the Omicron variant. In contrast, another study performed DMS with yeast surface display and analyzed RBD expression and binding of RBD with several concentrations of ACE2 (21). Yeast screening has advantages in terms of library size and the ability to restrict incorporation of multiple mutants due to the exclusive nature of different plasmids. The hemagglutinin (HA)-tagged spike protein library encompassed all 20 amino acid substitutions in the RBD (encompassing P329 to G538) of the original SARS-CoV-2 Wuhan strain spike protein and was transfected in Expi293F cells in a manner where cells typically acquire no more than a single variant ( 20). After infection of library cells by ACE2-harboring viruses in the presence or absence of neutralizing agents, infected GFP-positive cells and control GFP-negative cells were harvested with fluorescence-activated cell sorting (FACS), RNA was extracted, and the library was sequenced ( Fig. 6A). The resulting spike protein-expressing cells constituted approximately 15% of transfected cells, which is a reasonable rate to avoid multiple library induction ( 22). For infectivity analysis, ACE2-harboring viruses were titrated to induce infection in 2 to 3% of the cells in consideration of the detection range and library complexity (fig. S5B). To analyze escape ability, ACE2-harboring viruses and neutralization agents were optimized to observe the reduction of infectivity from 10% to 3% (fig. S5B and C). DMS experiments were performed in duplicate, which produced similar results (R2 = ~0.5) as was the case in previous studies conducted on HIV and influenza pathology with library viruses ( 23, 24) (fig. S6A). We also performed DMS for spike protein expression assessed by the staining of HA tagged to N-terminal full-length spike protein. ( 7), and both showed similar or better neutralization against Omicron (fig. S2). Wild type ACE2-Fc (spanning residues 18-740 with the collectrin domain) neutralized Omicron better than Wuhan, similar to the Alpha or Delta variants, which is consistent with a previous report ( 9). Nevertheless, engineered ACE2 molecules maintain an advantage for Omicron over wild type ACE2 decoy ( Fig. 3B). In contrast, engineered ACE2 treatment significantly rescued these mice (p=0.035, Fig. 5E). These data indicate that engineered ACE2 remains active in neutralizing the Omicron variant in vitro and in vivo. In contrast, the removal of NTD mutations from Omicron increased susceptibility to vaccine neutralization (Fig. 2D). Convalescent serum from individuals infected before the Delta variant wave (December 2020 through January 2021) showed 19.3 and 17.8-fold reduction compared with parental virus or Alpha. On the other hand, serum samples collected from individuals infected during or after the Delta variant wave (August 2021 through October 2021) exhibited 9.5 and 15.4-fold reduction compared with the parental virus or Delta, respectively.

This page provides regular updates on COVID prevalence based on analysis of wastewater data collected from more than 150 buildings on campus by Stanford's ...

Wastewater information is available sooner than information from clinical testing, which means that monitoring SARS-CoV-2 in wastewater can serve as an early indicator of increasing or decreasing COVID-19 infections in the community. In addition, results for genes present in Omicron BA.1 (Del143-145) and Omicron BA.2 (LPPA24S) are shown. The two blue lines on this graph represent the two genes (N, light blue and S, medium blue) that are present in every COVID variant, representing the total overall presence of COVID RNA in the sample. SARS-CoV-2 (the virus that causes COVID-19) is shed in feces by infected individuals and can be measured in wastewater. Collection and analysis at the Stanford site began in July 2021. When reviewing the graph below, it is important to look at the overall, sustained trends, instead of measurements on any given day.

Unvaccinated people threaten the safety of the vaccinated even when SARS-Cov-2 vaccination rates are high, according to a new modelling study published in ...

The authors' findings remained stable even when they modelled lower levels of vaccine effectiveness for prevention of infection, such as in those who have not received a booster dose or with new SARS-CoV-2 variants. When unvaccinated mixed with unvaccinated, the risk to vaccinated people was lower. "However, we found that the choices made by people who forgo vaccination contribute disproportionately to risk among those who do get vaccinated."

Researchers from the University of Toronto in Canada used a simple model to explore the effect of mixing between unvaccinated and vaccinated people to ...

KCNA cites Kim as saying North Korea will “continue to take steps to further bolster and develop its nuclear forces at the maximum speed.” Jack Dorsey, who had stepped from the post of CEO last year, backed the idea of Musk taking over. Pitching himself as a free-speech absolutist, Musk has voiced his opinion on the moderation by the social media giant. China's capital Beijing on Tuesday started testing most of its nearly 22 million residents for Covid-19, swiftly expanding mass tests from one district, Chaoyang, to many more areas within 24 hours amid a spreading outbreak and fears of a Shanghai-style lockdown. "Risk among unvaccinated people cannot be considered self-regarding. "Considerations around equity and justice for people who do choose to be vaccinated, as well as those who choose not to be, need to be considered in the formulation of vaccination policy," they said.