Vaccine Escape Mutants Research Articles

Prevalence of Genotypic Resistance Mutations in Patients with Chronic Hepatitis B (HBV) Treated with Entecavir and Tenofovir in Two Reference Centers in the North and Northeast of Brazil

Mutations of genotypic resistance to nucleotide analogues Entecavirand Tenofovirhave been described in patients undergoing treatment and virgins for hepatitis B virus. The present study demonstrated in a sample of 263 patients with chronic HBV from the North and Northeast of Brazil, a mutation rate of resistance to nucleotide analogues of 3.8% (10). Of the 10 patients who had genotypic resistance mutations, only 1 had no genotypic resistance mutation for the first line treatment for hepatitis B, entecavir and tenofovir.Due to the emergence of vaccine escape mutations and resistance mutations to antiviral treatment, and the severity of liver disease caused by HBV, screening for genetic mutations is important due to the impact on therapeutic management.

Phylogenetic and drug- and vaccine-resistance profiles of Hepatitis B Virus among children with HIV co-infection in Pakistan.

HIV-1 and hepatitis B virus (HBV) share common routes of transmission and therefore co-infection is common. In 2019, an HIV-1 outbreak that resulted in >1000 children being infected, predominantly through nosocomial transmission, occurred in Sindh, Pakistan. We conducted a phylogenetic and drug resistance analysis of the HBV Reverse Transcriptase (RT) gene in children with HIV-1 and HBV co-infection. Blood samples were collected from 321 children with HIV who were recruited as part of a study to investigate the HIV-1 outbreak. All samples were tested for HBV surface antigen (HBsAg) using an ELISA assay, and positive samples were used to amplify and sequence the HBV RT gene. The phylogenetic relationship between sequences was analyzed, and drug- and vaccine- resistance mutations in the RT gene were explored. Of 321 samples, 23% (n=75) were positive for HBsAg on ELISA. Phylogenetic analysis of the sequences revealed that 63.5% of HBV sequences were sub-genotype D1, while the rest were sub-genotype D2. Cluster analysis revealed grouping of sub-genotype D1 sequences exclusively with Pakistani sequences, while clustering of sub-genotypes D2 predominantly with global sequences. The 236Y mutation associated with resistance to tenofovir was observed in 2.8% of HBV sequences. Additionally, seven vaccine escape mutations were observed, the most common being 128V. Our study suggests ongoing transmission of HBV D1 and D2 sub-genotypes in the HIV-1 co-infected population, likely nosocomially, given common routes of HVB and HIV-1 transmission. The prevalence of major HBV drug- and vaccine-resistant mutations remains low. Surveillance for further transmissions and the possible emergence of major drug- or vaccine-resistant variants is required.

Neutralization of hepatitis B virus with vaccine-escape mutations by hepatitis B vaccine with large-HBs antigen

Although the current hepatitis B (HB) vaccine comprising small-HBs antigen (Ag) is potent and safe, attenuated prophylaxis against hepatitis B virus (HBV) with vaccine-escape mutations (VEMs) has been reported. We investigate an HB vaccine consisting of large-HBsAg that overcomes the shortcomings of the current HB vaccine. Yeast-derived large-HBsAg is immunized into rhesus macaques, and the neutralizing activities of the induced antibodies are compared with those of the current HB vaccine. Although the antibodies induced by the current HB vaccine cannot prevent HBV infection with VEMs, the large-HBsAg vaccine-induced antibodies neutralize those infections. The HBV genotypes that exhibited attenuated neutralization via these vaccines are different. Here, we show that the HB vaccine consisting of large-HBsAg is useful to compensate for the shortcomings of the current HB vaccine. The combined use of these HB vaccines may induce antibodies that can neutralize HBV strains with VEMs or multiple HBV genotypes.

Human ACE2 Peptide-Attached Plasmonic-Magnetic Heterostructure for Magnetic Separation, Surface Enhanced Raman Spectroscopy Identification, and Inhibition of Different Variants of SARS-CoV-2 Infections.

The emergence of Alpha, Beta, Gamma, Delta, and Omicron variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for several million deaths up to now. Because of the huge amount of vaccine escape mutations in the spike (S) protein for different variants, the design of material for combating SARS-CoV-2 is very important for our society. Herein, we report on the design of a human angiotensin converting enzyme 2 (ACE2) peptide-conjugated plasmonic-magnetic heterostructure, which has the capability for magnetic separation, identification via surface enhanced Raman spectroscopy (SERS), and inhibition of different variant SARS-CoV-2 infections. In this work, plasmonic-magnetic heterostructures were developed using the initial synthesis of polyethylenimine (PEI)-coated Fe3O4-based magnetic nanoparticles, and then gold nanoparticles (GNPs) were grown onto the surface of the magnetic nanoparticles. Experimental binding data between ACE2-conjugated plasmonic-magnetic heterostructures and spike-receptor-binding domain (RBD) show that the Omicron variant has maximum binding ability, and it follows Alpha < Beta < Gamma < Delta < Omicron. Our finding shows that, due to the high magnetic moment (specific magnetization 40 emu/g), bioconjugated heterostructures are capable of effective magnetic separation of pseudotyped SARS-CoV-2 bearing the Delta variant spike from an infected artificial nasal mucus fluid sample using a simple bar magnet. Experimental data show that due to the formation of huge "hot spots" in the presence of SARS-CoV-2, Raman intensity for the 4-aminothiolphenol (4-ATP) Raman reporter was enhanced sharply, which has been used for the identification of separated virus. Theoretical calculations using finite-difference time-domain (FDTD) simulation indicate that, due to the "hot spots" formation, a six orders of magnitude Raman enhancement can be observed. A concentration-dependent inhibition efficiency investigation using a HEK293T-human cell line indicates that ACE2 peptide-conjugated plasmonic-magnetic heterostructures have the capability of complete inhibition of entry of different variants and original SARS-CoV-2 pseudovirions into host cells.

Comparative analysis of hepatitis B virus infections in blood donors born before and after the implementation of universal HBV vaccination in southern China.

In China, the vaccinated blood donors have rapidly increased by recent years, which may impact blood safety. The true prevalence of HBV between vaccinated blood donors and non-vaccinated blood donors should be explored. The samples of blood donors were collected and detected for serologic markers of HBV in the Shenzhen Blood Centre (SZBC). The discrepant results were tested with commercial electrochemiluminescence immunoassay (ELCI) for HBsAg, anti-HBs, HBeAg, Anti-HBe and Anti-HBc, alternative MPX ID NAT, nested PCR, and a quantitative real-time polymerase chain reaction (qPCR) assay for HBV DNA. The serological and molecular characteristics of HBV infected blood donors were analysed, and the effects on blood safety for donors born before and after the implementation of universal HBV vaccination were compared. Out of 242 presumed HBV infected donors from 26 318 donations, 131 (0.49%, [95% CI, 0.43-0.59]) chronic HBV infections (CHB, HBsAg detected with or without DNA), 58 (0.22%, [95% CI, 0.17-0.28]) occult hepatitis B infections (OBI, HBsAg not detected, assume anti-HBc positive and/or anti-HBs with HBV DNA) and 3 (0.011%, [95% CI, 0.0023-0.033]) window period (WP) infections were confirmed respectively. There were 28 CHBs (0.44%), 7 OBIs (0.11%) and 1 WP (0.016%) from vaccinated blood donor and 103 CHBs (0.52%), 51 OBIs (0.26%) and 2 WPs (0.01%) from non-vaccinated blood donor. The HBV+ (CHBs, OBIs and WPs) rate (0.56%) in vaccinated donors was lower than in non-vaccinated donors (0.78%, p < 0.05). The HBsAg titers of vaccinated infected blood donors (Median: 128.8IU/ml) were much higher than non-vaccinated infected blood donors (58.4IU/ml). The OBI yield rates in the vaccinated blood donors was significantly lower than the non-vaccinated blood donors (p < 0.05). There 102/124 (82.3%) samples were genotype B, 22/124 (17.7%) were genotype C respectively. There was no significant difference in the distribution of genotype between non-vaccinated blood donors (B/C, 86/17) and vaccinated blood donors (B/C, 23/6; p > 0.05). High frequency of vaccine escape mutations M133L (32.4%) and E164G in S region of genotype B strains and substitution L175S (40.9%) related to vaccine escape in S region of genotype C strains were identified. The universal HBV vaccination program markedly reduces the risk of HBV infection in blood donors, and provides a significant guarantee for the safety of blood transfusion. Several important mutations detected related vaccine escape and notable mutations needed further investigated.

Vaccination strategies when vaccines are scarce: on conflicts between reducing the burden and avoiding the evolution of escape mutants.

When vaccine supply is limited but population immunization urgent, the allocation of the available doses needs to be carefully considered. One aspect of dose allocation is the time interval between the first and the second injections in two-dose vaccines. By stretching this interval, more individuals can be vaccinated with the first dose more quickly, which can be beneficial in reducing case numbers, provided a single dose is sufficiently effective. On the other hand, there has been concern that intermediate levels of immunity in partially vaccinated individuals may favour the evolution of vaccine escape mutants. In that case, a large fraction of half-vaccinated individuals would pose a risk—but only if they encounter the virus. This raises the question whether there is a conflict between reducing the burden and the risk of vaccine escape evolution or not. We develop an SIR-type model to assess the population-level effects of the timing of the second dose. Trade-offs can occur both if vaccine escape evolution is more likely or if it is less likely in half-vaccinated than in unvaccinated individuals. Their presence or absence depends on the efficacies for susceptibility and transmissibility elicited by a single dose.

Oral antivirals for the prevention and treatment of SARS-CoV-2 infection.

Vaccines and antivirals are the classical weapons deployed to contain, prevent, and treat life-threatening viral illnesses. Specifically, for SARS-CoV-2 infection, vaccines protect against severe COVID-19 disease manifestations and complications. However, waning immunity and emergence of vaccine escape mutants remains a growing threat. This is highlighted by the current surge of the omicron COVID-19 variant. Thus, there is a race to find treatment alternatives. We contend that oral small molecule antivirals that halt SARSCoV- 2 infection are essential. Compared to currently available monoclonal antibodies and remdesivir, where parenteral administration is required, oral antivirals offer treatments in an outpatient setting with dissemination available on a larger scale. In response to this need at 2021's end, regulatory agencies provided emergency use authorization for both molnupiravir and nirmatrelvir. These medicines act on the viral polymerase and protease, respectively. Each is given for 5 days and can reduce disease progression by 30% and 89%, respectively. The advent of additional oral antivirals, the assessment of combination therapies, the formulation of extended-release medications, and their benefit for both early treatment and prophylaxis will likely transform the landscape of the COVID-19 pandemic.

Containment strategies for COVID-19 in India: lessons from the second wave

ABSTRACT Introduction The COVID-19 pandemic in India has resulted in mass destruction in the form of second wave.Indian citizens and government were badly affected and were left constrained with basic medical facilities in treating the heavy load of patients. The possibility of reemergence of virulent strains of SARS-CoV-2 still exists. Area covered In this article, we tend to discuss why India is at high risk to be to be affected by the other waves and what strategies could be implemented to contain the viral spread. It provides these insights with reference to the gaps and the lessons learnt from the second wave along with the possible solutions to tackle these problems that were not effectively handled during the previous episodes of viral spread. We propose strategies for implementing effective vaccination programs, focus on speeding up different ways of diagnosis, management of essential hospital aids, prevention from vaccine escape mutant strains and implementation of COVID-appropriate behavior in rural areas of India. Expert opinion This article has significance to the researchers and government officials in understanding the gaps that led to COVID-19 second wave in India and provides an opportunity to improve on certain areas for handling the future waves with more vigilance. Abbreviations: COVID-19 – Coronavirus disease 2019; SARS-COV-2 – severe acute respiratory syndrome – Coronavirus 2; δ – Delta variant; δ+ – Delta plus variant; WHO – World Health Organization; RT –PCR – Reverse transcription PCR; IFN-1 – Interferon 1; VOCs – Variants of concern; HCWs – healthcare workers

Emerging Vaccine-Breakthrough SARS-CoV-2 Variants.

The surge of COVID-19 infections has been fueled by new SARS-CoV-2 variants, namely Alpha, Beta, Gamma, Delta, and so forth. The molecular mechanism underlying such surge is elusive due to the existence of 28 554 unique mutations, including 4 653 non-degenerate mutations on the spike protein. Understanding the molecular mechanism of SARS-CoV-2 transmission and evolution is a prerequisite to foresee the trend of emerging vaccine-breakthrough variants and the design of mutation-proof vaccines and monoclonal antibodies. We integrate the genotyping of 1 489 884 SARS-CoV-2 genomes, a library of 130 human antibodies, tens of thousands of mutational data, topological data analysis, and deep learning to reveal SARS-CoV-2 evolution mechanism and forecast emerging vaccine-breakthrough variants. We show that prevailing variants can be quantitatively explained by infectivity-strengthening and vaccine-escape (co-)mutations on the spike protein RBD due to natural selection and/or vaccination-induced evolutionary pressure. We illustrate that infectivity strengthening mutations were the main mechanism for viral evolution, while vaccine-escape mutations become a dominating viral evolutionary mechanism among highly vaccinated populations. We demonstrate that Lambda is as infectious as Delta but is more vaccine-resistant. We analyze emerging vaccine-breakthrough comutations in highly vaccinated countries, including the United Kingdom, the United States, Denmark, and so forth. Finally, we identify sets of comutations that have a high likelihood of massive growth: [A411S, L452R, T478K], [L452R, T478K, N501Y], [V401L, L452R, T478K], [K417N, L452R, T478K], [L452R, T478K, E484K, N501Y], and [P384L, K417N, E484K, N501Y]. We predict they can escape existing vaccines. We foresee an urgent need to develop new virus combating strategies.

First detection of SARS-CoV-2 lineage A.27 in Sardinia, Italy.

Multiple variants of SARS-CoV-2, since the end of 2020 have emerged in many geographical areas and are currently under surveillance worldwide highlighting the continuing need for genomic monitoring to detect variants previously not yet identified. In this study, we used whole-genome sequencing (WGS) and phylogenetic analysis to investigate A.27 lineage SARS-CoV-2 from Sardinia, Italy. The Italian A.27 lineage genomes from Sardinia appeared related in a clade with genomes from France. Among the key mutations identified in the spike protein, the N501Y and the L452R deserve attention as considered likely vaccine escape mutations. Additional mutations were also here reported. A combination of features could explain our data such as SARS-CoV-2 genetic variability, viral dynamics, the human genetic diversity of Sardinian populations, the island context probably subjected to different selective pressures. Molecular and genomic investigation is essential to promptly identify variants with specific mutations with potential impact on public health and vaccine formulation.

Profile of Hepatitis B Virus Mutations Associated with HBsAg-Negative Disease in Patients of Hemodialysis Centers

The aim of this study was to characterize mutations in the hepatitis B virus (HBV) genome associated with HBsAg-negative form of the disease in patients receiving hemodialysis replacement therapy. Materials and methods. We used blood plasma samples obtained from hemodialysis centers in St. Petersburg, Russia – 173 patients and 108 patients from Belgrade, Republic of Serbia. The samples were examined for the presence of serological (HBsAg, antibodies anti-HBs IgG, anti-HBcore IgG) and molecular-genetic (HBV DNA) markers of HBV followed by whole-genome sequencing and determination of clinically significant virus mutations. Results and discussion. Antibodies to hepatitis B were detected in 7.5 % and 11.1 % of patients from St. Petersburg and Belgrade, respectively. HBsAg was identified only in 1.1 % of cases in the group from Russia and in 0.9 % of cases in the group from Serbia. HBV DNA was determined in 2.8 % of the studied samples from both, patients from Saint-Petersburg and Belgrade. Phylogenetic analysis of 9 viral isolates showed that genotype D virus (88.9 %) prevailed as compared to genotype A (11.1 %) in the examined group. Among the samples obtained from patients from St. Petersburg, four belonged to the D2 sub-genotype, one to the D3 genotype. Four samples obtained from Belgrade patients belonged to different sub-genotypes – D1, D2, D3, A2, respectively. When analyzing the nucleotide sequences of the HBV genomes, mutations in the MHR region were detected in all cases, but only in HBsAg-negative isolates, mutations were revealed in the region of 124–147 amino acids, including mutations P120T, R122K, A128V, Q129R, M133I, G145R affecting the recognition of HBsAg by anti-HBs antibodies and associated with the resistance of the virus to the vaccine. The results of this study indicate that transmission of blood-borne viral hepatitis agent in the hemodialysis departments of the Russian Federation and the Republic of Serbia still exists. The prevalence of the latent chronic hepatitis B, coupled with the presence of vaccine escape mutations in all identified cases, indicates the need to pay close attention to the occurrence of the virus mutant variants in hemodialysis centers.

HiSpike Method for High-Throughput Cost Effective Sequencing of the SARS-CoV-2 Spike Gene.

The changing nature of the SARS-CoV-2 pandemic poses unprecedented challenges to the world's health systems. Emerging spike gene variants jeopardize global efforts to produce immunity and reduce morbidity and mortality. These challenges require effective real-time genomic surveillance solutions that the medical community can quickly adopt. The SARS-CoV-2 spike protein mediates host receptor recognition and entry into the cell and is susceptible to generation of variants with increased transmissibility and pathogenicity. The spike protein is the primary target of neutralizing antibodies in COVID-19 patients and the most common antigen for induction of effective vaccine immunity. Tight monitoring of spike protein gene variants is key to mitigating COVID-19 spread and generation of vaccine escape mutants. Currently, SARS-CoV-2 sequencing methods are labor intensive and expensive. When sequence demands are high sequencing resources are quickly exhausted. Consequently, most SARS-CoV-2 strains are sequenced in only a few developed countries and rarely in developing regions. This poses the risk that undetected, dangerous variants will emerge. In this work, we present HiSpike, a method for high-throughput cost effective targeted next generation sequencing of the spike gene. This simple three-step method can be completed in < 30 h, can sequence 10-fold more samples compared to conventional methods and at a fraction of their cost. HiSpike has been validated in Israel, and has identified multiple spike variants from real-time field samples including Alpha, Beta, Delta and the emerging Omicron variants. HiSpike provides affordable sequencing options to help laboratories conserve resources for widespread high-throughput, near real-time monitoring of spike gene variants.

Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance.

The latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has ushered panic responses around the world due to its contagious and vaccine escape mutations. The essential infectivity and antibody resistance of the SARS-CoV-2 variant are determined by its mutations on the spike (S) protein receptor-binding domain (RBD). However, a complete experimental evaluation of Omicron might take weeks or even months. Here, we present a comprehensive quantitative analysis of Omicron’s infectivity, vaccine breakthrough, and antibody resistance. An artificial intelligence (AI) model, which has been trained with tens of thousands of experimental data and extensively validated by experimental results on SARS-CoV-2, reveals that Omicron may be over 10 times more contagious than the original virus or about 2.8 times as infectious as the Delta variant. On the basis of 185 three-dimensional (3D) structures of antibody–RBD complexes, we unveil that Omicron may have an 88% likelihood to escape current vaccines. The U.S. Food and Drug Administration (FDA)-approved monoclonal antibodies (mAbs) from Eli Lilly may be seriously compromised. Omicron may also diminish the efficacy of mAbs from AstraZeneca, Regeneron mAb cocktail, Celltrion, and Rockefeller University. However, its impacts on GlaxoSmithKline’s sotrovimab appear to be mild. Our work calls for new strategies to develop the next generation mutation-proof SARS-CoV-2 vaccines and antibodies.

Omicron and its implications in dentistry

Due to its contagiousness and vaccine-escape mutations, the latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has sparked worldwide fear. The SARS-CoV-2 variant's critical infectivity and antibody resistance are determined by mutations in the Spike (S) protein receptor-binding domain (RBD). A comprehensive experimental study of Omicron, on the other hand, could take weeks or even months. For a hygienic and healthy work environment and treatment modality, we propose a standard operating protocol and protocols that all dental practitioners and staff should adhere to.

Brain cross‐protection against SARS‐CoV‐2 variants by a lentiviral vaccine in new transgenic mice

COVID‐19 vaccines already in use or in clinical development may have reduced efficacy against emerging SARS‐CoV‐2 variants. In addition, although the neurotropism of SARS‐CoV‐2 is well established, the vaccine strategies currently developed have not taken into account protection of the central nervous system. Here, we generated a transgenic mouse strain expressing the human angiotensin‐converting enzyme 2, and displaying unprecedented brain permissiveness to SARS‐CoV‐2 replication, in addition to high permissiveness levels in the lung. Using this stringent transgenic model, we demonstrated that a non‐integrative lentiviral vector, encoding for the spike glycoprotein of the ancestral SARS‐CoV‐2, used in intramuscular prime and intranasal boost elicits sterilizing protection of lung and brain against both the ancestral virus, and the Gamma (P.1) variant of concern, which carries multiple vaccine escape mutations. Beyond induction of strong neutralizing antibodies, the mechanism underlying this broad protection spectrum involves a robust protective T‐cell immunity, unaffected by the recent mutations accumulated in the emerging SARS‐CoV‐2 variants.

Post-Vaccination Coronavirus Disease 2019: A Case-Control Study and Genomic Analysis of 119 Breakthrough Infections in Partially Vaccinated Individuals.

BackgroundPost-vaccination infections challenge the control of the coronavirus disease 2019 (COVID-19) pandemic.MethodsWe matched 119 cases of post-vaccination severe acute respiratory syndrome coronavirus 2 infection with BNT162b2 mRNA or ChAdOx1 nCOV-19 to 476 unvaccinated patients with COVID-19 (September 2020–March 2021) according to age and sex. Differences in 60-day all-cause mortality, hospital admission, and hospital length of stay were evaluated. Phylogenetic, single-nucleotide polymorphism (SNP), and minority variant allele (MVA) full-genome sequencing analysis was performed.ResultsOverall, 116 of 119 cases developed COVID-19 post–first vaccination dose (median, 14 days). Thirteen of 119 (10.9%) cases and 158 of 476 (33.2%) controls died (P < .001), corresponding to the 4.5 number needed to treat (NNT). Multivariably, vaccination was associated with a 69.3% (95% confidence interval [CI]: 45.8 to 82.6) relative risk (RR) reduction in mortality. Similar results were seen in subgroup analysis for patients with infection onset ≥14 days after first vaccination and across vaccine subgroups. Hospital admissions (odds ratio, 0.80; 95% CI: .51 to 1.28) and length of stay (–1.89 days; 95% CI: –4.57 to 0.78) were lower for cases, while cycle threshold values were higher (30.8 vs 28.8, P = .053). B.1.1.7 was the predominant lineage in cases (100 of 108, 92.6%) and controls (341 of 446, 76.5%). Genomic analysis identified 1 post-vaccination case that harbored the E484K vaccine-escape mutation (B.1.525 lineage).ConclusionsPrevious vaccination reduces mortality when B.1.1.7 is the predominant lineage. No significant lineage-specific genomic changes during phylogenetic, SNP, and MVA analysis were detected.

Molecular Epidemiology of SARS-CoV-2 in Healthcare Workers and Identification of Viral Genomic Correlates of Transmissibility and Vaccine Break Through Infection: A Retrospective Observational Study From a Cancer Hospital in Eastern India

Background: Despite COVID vaccination with COVISHIELD vaccine (ChAdOx1 ncov-19) large number of healthcare workers (HCWs) was getting infected in wave-2 of the pandemic in a cancer hospital in eastern part of India.Methods: Retrospective observational study of HCWs. Whole genome sequencing of SARS CoV-2 using Illumina NovaSeq was done. Mutations from both waves were compared to identify genomic correlates of transmissibility and vaccine breakthrough infections.Findings: Vaccine breakthrough infections were seen in 127 HCWs out of 1,806 fully vaccinated staff (7.03%). Median number of HCWs infected per day in wave-1 was 0.92 versus 3.25 in wave-2. Majority of wave-1 samples belonged to B.1 and B.1.1 lineage. Variant of concern- Delta variant (90%), and variant of interest- Kappa variant (10%), was seen in only wave-2 samples. Total mutation observed in wave-2 samples (median = 44) was 1.8 times than wave-1 sample (median=24). Same trend was observed in coding mutation count. Spike protein in wave-2 samples contain 13 non-synonymous mutation as compared to 8 seen in wave-1 samples. E484Q- vaccine escape mutant was detected in five samples of wave-2; T478K – highly infectious mutation was seen in 31 samples of wave-2. We identified a novelcoding disruptive in-frame deletion (c.467_472delAGTTCA, p.Glu156_Arg158delinsGly) in the Spike protein. This mutation was seen only in wave-2 (78%, n=39) samples. The mutation overlaps the spike protein NTD domain and is present in the supersite b-hairpin.Interpretation: We noted that vaccine breakthrough infections (although mostly mild) were not uncommon and occurred despite two doses of COVISHIELD vaccine. The potential causes of vaccine breakthrough infections, and the most optimal schedule for HCWs need to be investigated.Funding Information: Study was funded by the institutional research fund of Tata Medical Center, Kolkata, India.Declaration of Interests: None to declare. Ethics Approval Statement: The TMC-IRB approved the study on 10th October 2020. The memo number was 2020/Govt/33/IRB46.

Breakthrough HBV infection in a vaccinated child due to vaccine escape mutant

Breakthrough HBV infection in a vaccinated child due to vaccine escape mutant

Characterization of Antigen Escape Mutations in Chronic HBV-Infected Patients in Upper Egypt.

BackgroundMutations within the “a” determinant region (position 124–147) that is present in the major hydrophilic region (MHR, position 99–160) of the hepatitis B surface antigen (HBsAg) are associated with vaccine-escape, lack of diagnosis, and failure to hepatitis B immunoglobulin (HBIG) therapy. Data regarding the amino acid changes of “a” determinant region of HBsAg are limited in Egypt. The prevalence and mutations in this region among chronic HBV (CHB)-infected patients in Upper Egypt are not known.Material and MethodsBlood samples were collected from HBsAg-positive CHB-infected patients (n=123) admitted to Assiut University Hospitals. Serum samples were screened for HBsAg, HBeAg, anti-HBs and anti-HBe antibodies using commercially available ELISA kits. Viral load was determined by qPCR. In addition, mutational analysis was carried out targeting the HBV surface gene to determine the HBV genotype and vaccine escape mutations.ResultsSequencing analysis of HBV DNA revealed that genotype D is the major circulating type (81.3%), followed by genotype E (18.7%). Analysis of the HBV genome revealed that 103/123 (83.7%) patients showed wild-type sequences and 20/123 (16.3%) showed mutations in the HBsAg gene. Mutation in seventeen patients (17/20, 85%) showed only one mutation, and three patients showed two mutations (3/20, 15%) in the “a” determinant region. The observed mutations were T115S (3/20, 15%), P120T/S (3/20, 15%), T126S (1/20, 5%), Q129R (2/20, 10%), M133T (2/20, 10%), S143L (5/20, 25%), D144E/A (3/20, 15%), and G145R/A (4/20, 20%). Mutations in the “a” determinant region were detected in genotype D isolates only.ConclusionWe described for the first time the prevalence and characterization of vaccine escape mutants in CHB patients in Upper Egypt. Mutational analysis of the “a” determinant region revealed the presence of a wide spectrum of mutants in the circulating HBV isolates that could be a potential threat to HBV diagnosis, therapy success, and HBV vaccination program in Upper Egypt.

Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries

Recently, the SARS-CoV-2 variants from the United Kingdom (UK), South Africa, and Brazil have received much attention for their increased infectivity, potentially high virulence, and possible threats to existing vaccines and antibody therapies. The question remains if there are other more infectious variants transmitted around the world. We carry out a large-scale study of 506,768 SARS-CoV-2 genome isolates from patients to identify many other rapidly growing mutations on the spike (S) protein receptor-binding domain (RBD). We reveal that essentially all 100 most observed mutations strengthen the binding between the RBD and the host angiotensin-converting enzyme 2 (ACE2), indicating the virus evolves toward more infectious variants. In particular, we discover new fast-growing RBD mutations N439K, S477N, S477R, and N501T that also enhance the RBD and ACE2 binding. We further unveil that mutation N501Y involved in United Kingdom (UK), South Africa, and Brazil variants may moderately weaken the binding between the RBD and many known antibodies, while mutations E484K and K417N found in South Africa and Brazilian variants, L452R and E484Q found in India variants, can potentially disrupt the binding between the RBD and many known antibodies. Among these RBD mutations, L452R is also now known as part of the California variant B.1.427. Finally, we hypothesize that RBD mutations that can simultaneously make SARS-CoV-2 more infectious and disrupt the existing antibodies, called vaccine escape mutations, will pose an imminent threat to the current crop of vaccines. A list of most likely vaccine escape mutations is given, including S494P, Q493L, K417N, F490S, F486L, R403K, E484K, L452R, K417T, F490L, E484Q, and A475S. Mutation T478K appears to make the Mexico variant B.1.1.222 the most infectious one. Our comprehensive genetic analysis and protein-protein binding study show that the genetic evolution of SARS-CoV-2 on the RBD, which may be regulated by host gene editing, viral proofreading, random genetic drift, and natural selection, gives rise to more infectious variants that will potentially compromise existing vaccines and antibody therapies.