Insight into free energy and dynamic cross-correlations of residue for binding affinity of antibody and receptor binding domain SARS-CoV-2.

SARS-CoV-2 virus continues to evolve and mutate causing most of the mutated variants resist to many of the therapeutic monoclonal antibodies (mAbs). Despite several mAbs retained neutralizing capability for Omicron BA.1 and BA.2, reduction in neutralization potency was reported. Hence, effort of searching for mAb that is broader in neutralization breadth without losing the neutralizing ability is continued. MW06 was reported with capability in neutralizing most of the variants of concern (VOC) and it binds to the conserved region (left flank) near epitope mAb sotrovimab (S309). In this study, binding affinity of mAb MW06 and its cocktail formulation with MW05 for receptor binding domain (RBD) SARS-CoV-2 virus was investigated under molecular dynamics simulations (MDs). Binding free energies computed by Molecular Mechanics Generalised Born Surface Area (MM-GBSA) algorithm predicted the binding affinity of MW06 for RBD BA.1 (-53 kcal/mol) as strong as RBD wildtype (-58 kcal/mol) while deterioration was observed for RBD BA.2 (-43 kcal/mol). Alike S309 and MW06, simulated cocktail mAb (MW05 and MW06)-RBD interactions suggested the neutralizing capability of the cocktail formulation for RBD BA.1 and BA.2 reduced. Meanwhile, residue pairs that favour the communication between the mAb and RBD have been identified by decomposing the free energy per pairwise residue basis. Apart from understanding the effects of mutation occurred in the RBD region on human angiotensin-converting enzyme 2 (hACE2) binding, impact of heavily mutated RBD on mAb-RBD interactions was investigated in this study as well. In addition to energetic profile obtained from MDs, plotting the dynamics cross-correlation map of the mAb-RBD complex under elastic network model (ENM) was aimed to understand the cross-correlations between residue fluctuations. It allows simple and rapid analysis on the motions or dynamics of the protein residues of mAbs and RBD in complex. Protein residues having correlated motions are normally part of the structural domains of the protein and their respective motions and protein function are related. Motion of mutated RBD residues and mAb residues was less correlated while their respective interactions energy computed to be higher. The combined techniques of MDs and ENM offered simplicity in understanding dynamics and energy contribution that explain binding affinity of mAb-RBD complexes.

Comparison of viral inactivation methods on the characteristics of extracellular vesicles from SARS-CoV-2 infected human lung epithelial cells.

The interaction of SARS-CoV-2 infection with extracellular vesicles (EVs) is of particular interest at the moment. Studying SARS-CoV-2 contaminated-EV isolates in instruments located outside of the biosafety level-3 (BSL-3) environment requires knowing how viral inactivation methods affect the structure and function of extracellular vesicles (EVs). Therefore, three common viral inactivation methods, ultraviolet-C (UVC; 1350 mJ/cm2 ), ß-propiolactone (BPL; 0.005%), heat (56°C, 45 min) were performed on defined EV particles and their proteins, RNAs, and function. Small EVs were isolated from the supernatant of SARS-CoV-2-infected human lung epithelial Calu-3 cells by stepwise centrifugation, ultrafiltration and qEV size-exclusion chromatography. The EV isolates contained SARS-CoV-2. UVC, BPL and heat completely abolished SARS-CoV-2 infectivity of the contaminated EVs. Particle detection by electron microscopy and nanoparticle tracking was less affected by UVC and BPL than heat treatment. Western blot analysis of EV markers was not affected by any of these three methods. UVC reduced SARS-CoV-2 spike detectability by quantitative RT-PCR and slightly altered EV-derived ß-actin detection. Fibroblast migration-wound healing activity of the SARS-CoV-2 contaminated-EV isolate was only retained after UVC treatment. In conclusion, specific viral inactivation methods are compatible with specific measures in SARS-CoV-2 contaminated-EV isolates. UVC treatment seems preferable for studying functions of EVs released from SARS-CoV-2 infected cells.

Biosensors for Klebsiella pneumoniae with Molecularly Imprinted Polymer (MIP) Technique.

Nosocomial infection is one of the most important problems that occurs in hospitals, as it directly affects susceptible patients or patients with immune deficiency. Klebsiella pneumoniae (K. pneumoniae) is the most common cause of nosocomial infections in hospitals. K. pneumoniae can cause various diseases such as pneumonia, urinary tract infections, septicemias, and soft tissue infections, and it has also become highly resistant to antibiotics. The principal routes for the transmission of K. pneumoniae are via the gastrointestinal tract and the hands of hospital personnel via healthcare workers, patients, hospital equipment, and interventional procedures. These bacteria can spread rapidly in the hospital environment and tend to cause nosocomial outbreaks. In this research, we developed a MIP-based electrochemical biosensor to detect K. pneumoniae. Quantitative detection was performed using an electrochemical technique to measure the changes in electrical signals in different concentrations of K. pneumoniae ranging from 10 to 105 CFU/mL. Our MIP-based K. pneumoniae sensor was found to achieve a high linear response, with an R2 value of 0.9919. A sensitivity test was also performed on bacteria with a similar structure to that of K. pneumoniae. The sensitivity results show that the MIP-based K. pneumoniae biosensor with a gold electrode was the most sensitive, with a 7.51 (% relative current/log concentration) when compared with the MIP sensor applied with Pseudomonas aeruginosa and Enterococcus faecalis, where the sensitivity was 2.634 and 2.226, respectively. Our sensor was also able to achieve a limit of detection (LOD) of 0.012 CFU/mL and limit of quantitation (LOQ) of 1.61 CFU/mL.

Virus MIP-composites for SARS-CoV-2 detection in the aquatic environment.

SARS-CoV-2 is the virus responsible for causing the global COVID-19 pandemic. Identifying the presence of this virus in the environment could potentially improve the effectiveness of disease control measures. Environmental SARS-CoV-2 monitoring may become increasingly demanded in areas where the available testing methods are ineffective. In this study, we present an electrochemical polymer composites biosensor for measuring SARS-CoV-2 whole-virus particles in the environment. The sensitized layer was prepared from molecularly imprinted polymer (MIP) composites of inactivated SARS-CoV-2. Testing demonstrated increased sensor signaling with SARS-CoV-2 specifically, while lower responses were observed to the negative controls, H5N1 influenza A virus and non-imprinted polymers (NIPs). This sensor detected SARS-CoV-2 at concentrations as low as 0.1 fM in buffer and samples prepared from reservoir water with a 3 log-scale linearity.

Enhancing sensitivity of QCM for dengue type 1 virus detection using graphene-based polymer composites.

Graphene oxide-molecularly imprinted polymer composites (GO-MIP) have attracted significant attention as recognition materials in sensing due to their outstanding properties in terms of electrical and thermal conductivity, high mechanical modulus, and the comparably straightforward way to functionalize them. The aim of this study was to design a MIP-based sensor recognition material and enhance its sensitivity by blending it with GO for sensing a harmful dengue hemorrhagic fever pathogen, namely the dengue type 1 virus (DENV-1). Polymer composites comprising GO incorporated to an acrylamide (AAM)/methacrylic acid (MAA)/methyl methacrylate (MMA)/N-vinylpyrrolidone (VP) copolymer were synthesized and compared to the "pure" MIP, i.e., the copolymer without GO. The pure polymer revealed a zeta potential of + 9.9 ± 0.5 mV, whereas GO sheets prepared have a zeta potential of - 60.3 ± 2.7 mV. This results in an overall zeta potential of - 11.2 ± 0.2 mV of the composite. Such polymer composites seem appropriate to bind the positively charged DENV-1 particle (+ 42.2 ± 2.8 mV). GO-MIP coated onto 10-MHz quartz crystal microbalance (QCM) sensors indeed revealed two times sensitivity compared to sensors based on the pure MIP. Furthermore, GO-polymer composites revealed imprinting factors of up to 21, compared to 3 of the pure MIP. When plotting the sensor characteristic in a semilogarithmic way, the composite sensor shows the linear response to DENV-1 in the concentration range from 100 to 103 pfu mL-1. The corresponding limits of detection (S/N = 3) and quantification (S/N = 10) are 0.58 and 1.94 pfu mL-1, respectively. Furthermore, imprinted polymer composites selectively bind DENV-1 without significant interference: DENV-2, DENV-3, DENV-4, respectively, yield 13-16% of DENV-1 signal. The sensor requires only about 15-20 min to obtain a result.

Electrochemical Biosensor Based on Surface Imprinting for Zika Virus Detection in Serum.

Zika virus (ZIKV) is a flavivirus that was first identified in 1947. Initially, the virus was of little concern for health authorities given there were very few casualties among those suffering an infection. As such, only limited studies were performed on ZIKV. Recently, the viral infection has been linked to microcephaly in infants, which has prompted a dramatic increase in scientific interest in ZIKV research, including methods to allow for rapid virus identification. In this work we report the development of a new type of ZIKV electrochemical biosensor based on surface imprinted polymers and graphene oxide composites. The biosensor was used to detect ZIKV by measuring changes in the electrical signal with changing virus concentrations in buffer and serum using standard electrochemical techniques. The detection limit of our method is similar to the detection limit of the real-time quantitative reverse transcription PCR method.

Small-Molecule Dengue Virus Co-imprinting and Its Application as an Electrochemical Sensor.

Polymers can be synthesized to recognize small molecules. This is achieved by introducing the target molecule during monomer self-assembly, where they can be incorporated during cross-linking polymerization. Following additional pre-processing, the material obtained can then be applied as a sensing layer for these molecules in many applications. The sensitivity of the polymers depends on the "active sites" imprinted on the surface. Increasing the number of active sites on the polymers surface can be achieved by using nanoparticles as a platform to support and concentrate the molecules for imprinting. In this work, we report the first use of dengue virus as a supporting nanoparticle to make for a more effective polymer composite sensor for the detection of bisphenol A (BPA), which is an environmental contaminant. The dengue virus has a nanoparticle size of around 100 nm and its surface provides regions where lipids and hydrophobic compounds can bind, making it an ideal support. The mixing of BPA with dengue prior to monomer self-assembly led to imprinted polymer surfaces with much higher density BPA binding sites and a limit of detection of 0.1 pm. We demonstrate that a BPA-dengue co-imprinting polymer composite sensor shows a very high sensitivity for BPA, but with lower production costs and technical requirements than other comparable methods.

An influenza A virus agglutination test using antibody-like polymers.

Antibodies are commonly used in diagnostic routines to identify pathogens. The testing protocols are relatively simple, requiring a certain amount of a specific antibody to detect its corresponding pathogen. Antibody functionality can be mimicked by synthesizing molecularly imprinted polymers (MIPs), i.e. polymers that can selectively recognize a given template structure. Thus, MIPs are sometimes termed 'plastic antibody (PA)'. In this study, we have synthesized new granular MIPs using influenza A virus templates by precipitation polymerization. The selective binding of influenza A to the MIP particles was assessed and subsequently contrasted with other viruses. The affinities of influenza A virus towards the MIP was estimated based on an agglutination test by measuring the amount of influenza subtypes absorbed onto the MIPs. The MIPs produced using the H1N1 template showed specific reactivity to H1N1 while those produced using H5N1 and H3N2 templates showed cross-reactivity.

H5N1 Virus Plastic Antibody Based on Molecularly Imprinted Polymers.

Normally, antibodies against influenza A have been prepared from viable virus or an engineered strain in certain hosts or cultured media. Two factors concerning antibody production are obvious. The obtaining antibody that is a kind of biomolecule has to be handled carefully, e.g., to be kept in a refrigerator. Furthermore, when the virus strain is highly pathogenic, such as H5N1, antibody production has to be done carefully in a high-level biosafety lab. Here, we show how to produce an antibody against H5N1 from a polymeric material using inactivated virus which can be conducted in a low-level biosafety lab. The process is based on imprinting the whole virus on a polymer surface to form molecularly imprinted polymers (MIPs). The MIPs show some properties of H5N1 antibody as they recognize H5N1 and have some important antibody activity. The H5N1 MIPs are not to be considered biomaterial, so they can be stored at room temperature and thus do not need any special care.

A novel method for dengue virus detection and antibody screening using a graphene-polymer based electrochemical biosensor.

Dengue fever is a major disease that kills many people in the developing world every year. During early infection, a patient displays a high temperature without other signs. After this stage, and without proper treatment, serious damage to internal organs can happen, which occasionally leads to death. A rapid technique for the early detection of dengue virus (DENV) could reduce the number of fatalities. This study presents a new technique for the detection, classification and antibody screening of DENV based on electrochemical impedance spectroscopy (EIS). We found that the charge transfer resistance (Rct) of a gold electrode coated with graphene oxide reinforced polymer was influenced by virus type and quantity exposed on the surface. Molecular recognition capability established during the GO-polymer composite preparation was used to explain this observation. The linear dependence of Rct versus virus concentrations ranged from 1 to 2×103pfu/mL DENV with a 0.12 pfu/mL detection limit.

Design and Generation of Humanized Single-chain Fv Derived from Mouse Hybridoma for Potential Targeting Application.

Single-chain variable antibody fragments (scFvs) are attractive candidates for targeted immunotherapy in several human diseases. In this study, a concise humanization strategy combined with an optimized production method for humanizing scFvs was successfully employed. Two antibody clones, one directed against the hemagglutinin of H5N1 influenza virus, the other against EpCAM, a cancer biomarker, were used to demonstrate the validity of the method. Heavy chain (VH) and light chain (VL) variable regions of immunoglobulin genes from mouse hybridoma cells were sequenced and subjected to the construction of mouse scFv 3-D structure. Based on in silico modeling, the humanized version of the scFv was designed via complementarity-determining region (CDR) grafting with the retention of mouse framework region (FR) residues identified by primary sequence analysis. Root-mean-square deviation (RMSD) value between mouse and humanized scFv structures was calculated to evaluate the preservation of CDR conformation. Mouse and humanized scFv genes were then constructed and expressed in Escherichia coli. Using this method, we successfully generated humanized scFvs that retained the targeting activity of their respective mouse scFv counterparts. In addition, the humanized scFvs were engineered with a C-terminal cysteine residue (hscFv-C) for site-directed conjugation for use in future targeting applications. The hscFv-C expression was extensively optimized to improve protein production yield. The protocol yielded a 20-fold increase in production of hscFv-Cs in E. coli periplasm. The strategy described in this study may be applicable in the humanization of other antibodies derived from mouse hybridoma.

Self-assembled glucosamine monolayers as biomimetic receptors for detecting WGA lectin and influenza virus with a quartz crystal microbalance.

N-Acetylglucosamine (GlcNAc) is a natural ligand that interacts with the binding sites of wheat germ agglutinin (WGA) lectin. For immobilization, GlcNAc was linked to p-nitrophenol, and the nitro group was reduced and then bound to cysteine via two-step synthesis. Scanning tunneling microscopy studies revealed proper immobilization of the ligand on the gold surface of a quartz crystal microbalance (QCM) via the cysteine S-H bond as well as binding between GlcNAc and WGA. QCM measurements revealed that maximum sensitivity towards WGA can only be achieved when co-immobilizing one part ligand and 5,000 parts cysteine for steric reasons, because it allows binding of a protein monolayer on the surface. Langmuir-type treatment of the binding isotherm suggests two different binding ranges for WGA and the GlcNAc monolayer, because at concentrations of WGA below 1 µm the Gibbs energy for the binding process is one third higher than that at concentrations above this value. The same systems can be transferred to first proof-of-concept measurements with different strains of influenza A virus (H5N3, H5N1, H1N3) because GlcNAc is part of the oligosaccharide ligand responsible for the first binding step. Thus, it constitutes both a suitable tool for rapid analysis and the basis for future theoretical calculations of ligand-virus interactions.

Influenza A virus molecularly imprinted polymers and their application in virus sub-type classification.

In this work, we apply a molecular imprinting strategy as a screening protocol for different influenza A subtypes, namely H5N1, H5N3, H1N1, H1N3 and H6N1. Molecularly imprinted polymers for each of these subtypes lead to appreciable sensor characteristics on a quartz crystal microbalance leading to detection limits as low as 105 particles per ml. Selectivity studies indicate that each virus is preferably incorporated by its own MIP. Recognition in most cases is dominated by the neuraminidase residue rather than the hemagglutinin. Multivariate analysis shows that the sensor responses can be correlated with the differences in hemagglutinin and neuraminidase patterns from databases. This allows for virus subtype characterization and thus rapid screening.

Receptor recognition mechanism of human influenza A H1N1 (1918), avian influenza A H5N1 (2004), and pandemic H1N1 (2009) neuraminidase.

Influenza A neuraminidase (NA) is a target for anti-influenza drugs. The function of this enzyme is to cleave a glycosidic linkage of a host cell receptor that links sialic acid (Sia) to galactose (Gal), to allow the virus to leave an infected cell and propagate. The receptor is an oligosaccharide on the host cell surface. There are two types of oligosaccharide receptor; the first, which is found mainly on avian epithelial cell surfaces, links Sia with Gal by an α2,3 glycosidic linkage; in the second, found mainly on human epithelial cell surfaces, linkage is via an α2,6 linkage. Some researchers believe that NAs from different viruses show selectivity for each type of linkage, but there is limited information available to confirm this hypothesis. To see if the linkage type is more specific to any particular NA, a number of NA-receptor complexes of human influenza A H1N1 (1918), avian influenza A H5N1 (2004), and a pandemic strain of H1N1 (2009) were constructed using homology modeling and molecular dynamics simulation. The results show that the two types of receptor analogues bound to NAs use different mechanisms. Moreover, it was found that a residue unique to avian virus NA is responsible for the recognition of the Siaα2,3Gal receptor, and a residue unique to human virus NA is responsible for the recognition of Siaα2,6Gal. We believe that this finding could explain how NAs of different virus origins always possess some unique residues.

In silico screening of epidermal growth factor receptor (EGFR) in the tyrosine kinase domain through a medicinal plant compound database.

The unregulated epidermal growth factor receptor tyrosine kinase (ErbB1-TK or EGFR-TK) protein is involved in the proliferation of more than 50% of all cancer types. The reduction of EGFR-TK activity by small or medium-sized molecules has been proven to be an effective treatment for cancer. There is a widespread belief that Chinese medicinal herbs are active against several diseases, including various types of cancer. In this study, 29,960 compounds from the Chemiebase medicinal compound database were virtually screened against the EGFR-TK using AutoDock4.0, GOLD and GLIDE (XP). The results revealed eight potential hits: CAS nos. 104096-45-9, 112649-21-5, 113866-89-0, 142608-98-8, 142608-99-9, 144761-33-1, 155233-17-3 and 80510-05-0. These compounds have been reported to show anticancer activities in the literature. With the help of SiMMap and MOE interaction analysis, the protein-ligand interaction patterns between the functional groups of these compounds and the binding pocket residues were analyzed. Hydrogen bonding and hydrophobic forces are the main components of the interactions of these hits, similar to those observed for the known inhibitors erlotinib, gefitinib and AEE. The physicochemical filter indicates that compounds CAS nos. 104096-45-9 and 144761-33-1 are likely to be potential leads in the drug discovery process.

Surface molecular imprints of WGA lectin as artificial receptors for mass-sensitive binding studies.

Wheat germ agglutinin (WGA) lectin is a model compound for the interaction between viruses and cells during infection events and thus an interesting analyte for mass-sensitive sensing to study these interaction phenomena. Scanning tunneling microscopy studies reveal that surface molecular imprinting leads to cavities having the dimensions of WGA dimers. These reincorporate WGA from phosphate-buffered saline between 1 and 160 µg/ml. Whereas the quartz crystal microbalance (QCM) frequency for molecularly imprinted polymer (MIP)-coated electrodes decreases, indicating uptake of the analyte, their nonimprinted counterparts yield positive, concentration-dependent frequency shifts characteristic for slip of the analyte on the QCM surface. The MIPs achieve selectivity factors towards bovine serum albumin of roughly 4 at higher protein concentrations. Brunauer-Emmett-Teller analysis reveals that binding is favored by 29 kJ/mol until the adsorption of up to ten monolayers on the MIP, whereas above this range the value is lower. Together with the binding behavior of MIP and nonimprinted polymers, this indicates that the MIP acts as a nucleus for multilayer deposition onto the surface.

Intra-host diversities of the receptor-binding domain of stork faeces-derived avian H5N1 viruses and its significance as predicted by molecular dynamic simulation.

Virus evolution facilitates the emergence of viruses with unpredictable impacts on human health. This study investigated intra-host variations of the receptor-binding domain (RBD) of the haemagglutinin (HA) gene of the avian H5N1 viruses obtained from the 2004 and 2005 epidemics. The results showed that the mutation frequency of the RBD ranged from 0.3 to 0.6 %. The mutations generated one consensus and several minor populations. The consensus population of the 2004 epidemic was transmitted to the 2005 outbreak with increased frequency (39 and 45 %, respectively). Molecular dynamics simulation was applied to predict the significance of the variants. The results revealed that the consensus sequence (E218K/V248I) interacted unstably with sialic acid (SA) with an α2,6 linkage (SAα2,6Gal). Although the mutated K140R/E218K/V248I and Y191C/E218K/V248I sequences decreased the HA binding capacity to α2,3-linked SA, they were shown to bind α2,6-linked SA with increased affinity. Moreover, the substitutions at aa 140 and 191 were positive-selection sites. These data suggest that the K140R and Y191C mutations may represent a step towards human adaptation of the avian H5N1 virus.

Computer techniques for drug development from Thai traditional medicine.

Thailand has a vast number of plant species. Up to 3000 of them are believed by traditional Thai medicine to possess some biological activity with which researchers have attempted for many years to identify and formulate new drugs. Many chemical compounds from Thai plant species are identified and tested for biological activity that may enable them to be declared lead compounds in drug discovery. Modern methods of drug discovery are rarely used to rationalize and speed-up the process. Within this decade, the first structural database of Thai medicinal plants, Chemiebase, has been built as a platform for virtual screening, using knowledge from Thai traditional medicine. Although this effort is a promising protocol which can be used to validate Thai traditional medicine, there exists another problem that should be resolved before proceeding: It is almost impossible to trace the knowledge to its primary source. Thai traditional knowledge has been passed on orally or - less frequently - in ancient texts. We have built another database, the Thai Herbal Repository Access Initiative (THRAI) database, in order to compile the traditional knowledge into electronic format suitable for the drug design process. Three examples using data from these databases and other computer-aided drug discovery methods to rationalize Thai traditional medicine are presented here, starting with virtual screening exercised on anti-HIV-1 reverse transcriptase, anti-HIV-1 protease, anti-influenza A neuraminidase, and anti-cyclooxygenase (COX), candidates. The second example consists of the use of molecular modeling to propose drug mechanism for anti-tumor compounds. The last one is the study on toxicity assessment of some compounds from Thai medicinal plants.

Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin.

BACKGROUND: It is known that the highly pathogenic avian influenza A virus H5N1 binds strongly and with high specificity to the avian-type receptor by its hemagglutinin surface protein. This specificity is normally a barrier to viral transmission from birds to humans. However, strains may emerge with mutated hemagglutinin, potentially changing the receptor binding preference from avian to human-type. This hypothesis has been proven correct, since viral isolates from Vietnam and Thailand have been found which have increased selectivity toward the human cell receptor. The change in binding preference is due to mutation, which can be computationally modelled. The aim of this study is to further explore whether computational simulation could be used as a prediction tool for host type selectivity in emerging variants. RESULTS: Molecular dynamics simulation was employed to study the interactions between receptor models and hemagglutinin proteins from H5N1 strains A/Duck/Singapore/3/97, mutated A/Duck/Singapore/3/97 (Q222L, G224S, Q222L/G224S), A/Thailand/1(KAN-1)/2004, and mutated A/Thailand/1(KAN-1)/2004 (L129V/A134V). The avian receptor was represented by Sia alpha(2,3)Gal substructure and human receptor by Sia alpha(2,6)Gal. The glycoside binding conformation was monitored throughout the simulations since high selectivity toward a particular host occurs when the sialoside bound with the near-optimized conformation. CONCLUSION: The simulation results showed all hemagglutinin proteins used the same set of amino acid residues to bind with the glycoside; however, some mutations alter linkage preferences. Preference toward human-type receptors is associated with a positive torsion angle, while avian-type receptor preference is associated with a negative torsion angle. According to the conformation analysis of the bound receptors, we could predict the relative selectivity in accordance with in vitro experimental data when disaccharides receptor analogs were used.

An avian influenza H5N1 virus that binds to a human-type receptor.

Avian influenza viruses preferentially recognize sialosugar chains terminating in sialic acid-alpha2,3-galactose (SAalpha2,3Gal), whereas human influenza viruses preferentially recognize SAalpha2,6Gal. A conversion to SAalpha2,6Gal specificity is believed to be one of the changes required for the introduction of new hemagglutinin (HA) subtypes to the human population, which can lead to pandemics. Avian influenza H5N1 virus is a major threat for the emergence of a pandemic virus. As of 12 June 2007, the virus has been reported in 45 countries, and 312 human cases with 190 deaths have been confirmed. We describe here substitutions at position 129 and 134 identified in a virus isolated from a fatal human case that could change the receptor-binding preference of HA of H5N1 virus from SAalpha2,3Gal to both SAalpha2,3Gal and SAalpha2,6Gal. Molecular modeling demonstrated that the mutation may stabilize SAalpha2,6Gal in its optimal cis conformation in the binding pocket. The mutation was found in approximately half of the viral sequences directly amplified from a respiratory specimen of the patient. Our data confirm the presence of H5N1 virus with the ability to bind to a human-type receptor in this patient and suggest the selection and expansion of the mutant with human-type receptor specificity in the human host environment.