Development and characterization of a novel nanobody with SRMV neutralizing activity

Peste des petits ruminants (PPR) is an acute, contact infectious disease caused by the small ruminant morbillivirus (SRMV), and its morbidity in goats and sheep can be up to 100% with significant mortality. Nanobody generated from camelid animals such as alpaca has attracted wide attention because of its unique advantages compared with conventional antibodies. The main objective of this study was to produce specific nanobodies against SRMV and identify its characteristics. To obtain the coding gene of SRMV-specific nanobodies, we first constructed an immune phage-displayed library from the VHH repertoire of alpaca that was immunized with SRMV-F and -H proteins. By using phage display technology, the target antigen-specific VHHs can be obtained after four consecutive rounds of biopanning. Results showed that the size of this VHH library was 2.26 × 1010 CFU/mL and the SRMV-F and -H specific phage particles were greatly enriched after four rounds of biopanning. The positive phage clones were selected and sequenced, and total of five independent different sequences of SRMV-specific nanobodies were identified. Subsequently, the DNA fragments of the five nanobodies were cloned into E. coli BL21(DE3), respectively, and three of them were successfully expressed and purified. Specificity and affinity towards inactivated SRMV of these purified nanobodies were then evaluated using the ELISA method. Results demonstrated that NbSRMV-1-1, NbSRMV-2-10, and NbSRMV-1-21 showed no cross-reactivity with other antigens, such as inactivated BTV, inactivated FMDV, His-tag labeled protein, and BSA. The ELISA titer of these three nanobodies against inactivated SRMV was up to 1:1000. However, only NbSRMV-1-21 displayed SRMV neutralizing activity at a maximum dilution of 1:4. The results indicate that the nanobodies against SRMV generated in this study could be useful in future applications. This study provided a novel antibody tool and laid a foundation for the treatment and detection of SRMV.

Development of a monoclonal antibody recognizing novel linear neutralizing epitope on H protein of canine distemper virus vaccine strains (America-1 genotype)

Canine distemper virus (CDV) is an economically important virus responsible for canine distemper (CD), a highly contagious disease that afflicts various animal species worldwide. The hemagglutinin (H) protein is the major neutralizing target of virus. Therefore, it is often considered as immunogen to prepare neutralizing antibodies. The accurate identification of neutralizing epitope will provide important antigenic information and extend the knowledge of mechanisms of virus neutralization. In this study, we generated a neutralizing monoclonal antibody (mAb) 4C6 against CDV H protein, and defined the minimal linear epitope 238DIEREFDT245, which was highly conserved in America-1 genotype of CDV strains (vaccines). The mAb 4C6 could not react with a CDV strain that had two substitutions of D238Y and R241G in the epitope, which appeared in most CDV strains of the other genotypes. Besides, a few different amino acid mutations in the epitope were also included. Collectively, the epitope 238DIEREFDT245 was variable in the other genotypes of CDV strains. The epitope 238DIEREFDT245 was exposed to the surface of CDV H protein, showing good antigenicity. These data will provide insights into structure, function and antigenicity of H protein and lay the foundation for the development of diagnostic technologies and vaccine design for CDV.

Genetic Characterization of the H Gene of MeV Strains (H1, B3, and D4) Recently Circulated in Iran for Improving the Molecular Measles Surveillance in the National Measles Lab

Background

Despite decreasing the global burden of measles disease after the introduction of vaccination, measles remains one of the most devastating childhood diseases. Since genotype B3 is reported as a predominant Measles Virus (MeV) genotype recently, the current study aimed to better understand MeV genetic variation by analyzing the complete sequence of Hemagglutinin (H) gene associated with outbreaks of circulated genotypes in Iran.

Methods

Nine positive measles specimens were selected from three circulated different genotypes H1, B3, and D4. Two different regions of MeV RNA were detected by RT-PCR assay. Sequence data and phylogenetic trees were analyzed and constructed by MEGA X software program. Moreover, missense and silent mutations in critical positions of the MeV-H protein were investigated.

Results

The result of phylogenetic analysis from the C-terminus of the Nucleoprotein gene (NP-450) and the complete H gene revealed that the mean sequence diversity was 0.06%-0.08% and 0.04%, respectively. Genotype H1 had the highest mutation in this study; however, the substitutions in genotype B3 fundamentally occurred in critical epitopes. Moreover, genotype D4 was more stable than genotypes B3 and H1.

Conclusion

Mutations were investigated in the whole sequence of H protein. Moreover, the mutations that occur in the critical sites of the protein have an important effect on the pathogenicity of the virus. In this way, we were able to illustrate why genotype B3 is more transmissible than other measles genotypes and is the most important circulating genotype around the world.

HA1 (Hemagglutinin) quantitation for influenza A H1N1 and H3N2 high yield reassortant vaccine candidate seed viruses by RP-UPLC

The only effective measure to decrease morbidity and mortality caused by the influenza virus in the human population is worldwide vaccination. Vaccination produces neutralizing antibodies that target the HA1 subunit of the HA (hemagglutinin) protein and are strain specific. The effectiveness of new influenza vaccines are linked to two factors, the correct prediction of the circulating strains in the population in a particular season and the concentration of the HA1 protein in the vaccine formulation. With the advent of the licensing of quadrivalent vaccines, pharmaceutical manufacturers are under considerable pressure due to time constraints and dedicated resources to deliver 194-198 million doses (2020-2021 U.S. market) of vaccine. Considering the valuable resources needed to produce the influenza vaccine in a timely manner, the efficient quantitation of the HA1 protein (the main component in the influenza vaccine) is required. Currently the only method approved by regulatory agencies for quantitation of the HA antigen in vaccines is the single radial immunodiffusion assay (SRID), an antibody dependent assay that is not time efficient. Time efficient methods that are antibody independent e.g. reverse phase-high performance liquid chromatography (RP-HPLC) or size exclusion-HPLC (SE-HPLC) are available. An improved method implementing reverse phase-ultra performance liquid chromatography (RP-UPLC) has been developed to quantitate the HA1 protein antigen present in the high yield reassortant vaccine seed viruses from influenza A H1N1 and H3N2 subtypes harvested from inoculated embryonated chicken eggs. This method differentiates between high yield and lower yielding reassortants in order to select the best vaccine candidate seed virus with the highest growth 'in ovo'. This direct capability to monitor the HA1 concentration of potential reassortant seed viruses and to choose the best yielding HA influenza reassortant when faced with multiple viral seed candidates provides a major advantage on the industrial scale to the influenza vaccine process.

Molecular analysis of influenza A H1N1pdm09 virus circulating in Madhya Pradesh, India in the year 2017

Influenza A (H1N1) pdm09 emerged as a major public health problem in 2009. The virus has evolved since then and has acquired several mutations that are epidemiologically important. Viral hemagglutinin (HA) protein is crucial determinant for virus entry, antigenicity, and virulence. The information regarding amino acid substitutions in HA protein of viruses circulating in India during 2017 is lacking. We sequenced HA gene of Influenza A (H1N1) pdm09 detected in Central India and compared the amino acid sequences with present vaccine component and contemporary Influenza A (H1N1) pdm09 sequences. We observed 7 amino acid changes of which two (T508A and I510T) were novel to Central Indian strain. Further, the substitution of Aspartate by Glycine at 222, which is known to have clinical implications, was detected in sequences from western India. The phylogenetic analysis revealed that the circulating virus belonged to clade 6B.1. The appreciable acquired mutations by the virus are not important antigenically and the present vaccine provides effective protection. On the other hand, the amino acid substitutions may play important role in epidemiology; we suggest rigorous molecular monitoring and documentation for timely interventions.

Fine mapping and conservation analysis of linear B-cell epitopes of peste des petits ruminants virus hemagglutinin protein

Hemagglutinin protein (H), one of the two glycoproteins of peste des petits ruminants virus (PPRV), binds to its receptor on the host cell and acts as a major antigen that induces and confers highly protective immunity in the host. In order to delineate the epitopes on H protein, fine epitope mapping and conservation analysis of linear B-cell epitopes (BCEs) on PPRV H has been undertaken using biosynthetic peptides and rabbit anti-PPRV H sera. Thirteen linear BCEs were identified and their corresponding minimal motifs were located on the H protein of PPRV China/Tibet/Geg/07-30. Conservation analysis indicated that two of the 13 minimal motifs were conserved among 52 PPRV strains. Nine of the 13 peptides containing the minimal motifs were recognized using anti-PPRV serum from a goat immunized with PPRV vaccine strain Nigeria 75/1. Identified epitopes and their motifs improve our understanding of the antigenic characteristics of PPRV H and provide a basis for the development of epitope-based diagnostic assays and multiple epitopes vaccine.

Measles virus genetic evolution throughout an imported epidemic outbreak in a highly vaccinated population

Measles virus circulates endemically in African and Asian large urban populations, causing outbreaks worldwide in populations with up-to-95% immune protection. We studied the natural genetic variability of genotype B3.1 in a population with 95% vaccine coverage throughout an imported six month measles outbreak. From first pass viral isolates of 47 patients we performed direct sequencing of genomic cDNA. Whilst no variation from index case sequence occurred in the Nucleocapsid gene hyper-variable carboxy end, in the Hemagglutinin gene, main target for neutralizing antibodies, we observed gradual nucleotide divergence from index case along the outbreak (0% to 0.380%, average 0.138%) with the emergence of transient and persistent non-synonymous and synonymous mutations. Little or no variation was observed between the index and last outbreak cases in Phosphoprotein, Nucleocapsid, Matrix and Fusion genes. Most of the H non-synonymous mutations were mapped on the protein surface near antigenic and receptors binding sites. We estimated a MV-Hemagglutinin nucleotide substitution rate of 7.28 × 10-6 substitutions/site/day by a Bayesian phylogenetic analysis. The dN/dS analysis did not suggest significant immune or other selective pressures on the H gene during the outbreak. These results emphasize the usefulness of MV-H sequence analysis in measles epidemiological surveillance and elimination programs, and in detection of potentially emergence of measles virus neutralization-resistant mutants.

Identification of a natural recombination in the F and H genes of feline morbillivirus

Feline morbillivirus (FmoPV) has recently been identified in Hong Kong and Japan. FmoPV is considered to belong to the genus Morbillivirus, in the family Paramyxoviridae. In this study, the complete nucleotide sequences of three strains of FmoPV detected in cats in Japan were determined. Among the six genes in FmoPV; N, P/V/C, M, F, H and L, the P gene showed the highest polymorphism in the nucleotide and putative amino acid sequences among the FmoPV strains. There was no geographical association in terms of the FmoPV phylogeny; however, from extensive phylogenetic and recombination analyses, we found that one Japanese FmoPV strain, MiJP003, was a probable recombinant between two virus strains in the independent lineages found in Japan and Hong Kong, respectively. The recombination was considered to have occurred within the F and H genes. Such recombination is thought to be involved in the evolution of FmoPV.

A Combinatorial approach: To design inhibitory molecules on Hemagglutinin protein of H1N1 virus (Swine Flu)

The Hemagglutinin (HA) is a protein of influenza A virus. It is present on the surface of influenza A virus and it is a glycoprotein. The HA is identified as potential drug target. H1N1 thiazolides, proved to be a potent drug in the inhibition of H1N1 replication. It is also known as inhibitor of other strains of influenza A virus. Thiazolide drug represses viral HA's maturation at a level which exists just before the resistance from digestion of endoglycosidase-H and thereby it hampers, HA insertion in host membrane. Blocking the appropriate active site of hemagglutinin protein helps in the disease control. In the present work, we have generated diverse combinatorial library based ligands on known inhibitor thiazolides and they were used for virtual screening by Molegro virtual docker program. K-means clustering approach was used for finding new inhibitory molecules with more appropriate features. These resulted molecules are may be helpful in the treatment of swine flu and many other related diseases.