Effects of amino acid sequence changes on antibody-antigen interactions

Analysis of SARS-CoV-2 nucleocapsid protein sequence variations in ASEAN countries

BACKGROUND Nucleocapsid (N) protein is one of four structural proteins of SARS-CoV-2  which is known to be more conserved than spike protein and is highly immunogenic. This study aimed to analyze the variation of the SARS-CoV-2 N protein sequences in ASEAN countries, including Indonesia. METHODS Complete sequences of SARS-CoV-2 N protein from each ASEAN country were obtained from Global Initiative on Sharing All Influenza Data (GISAID), while the reference sequence was obtained from GenBank. All sequences collected from December 2019 to March 2021 were grouped to the clade according to GISAID, and two representative isolates were chosen from each clade for the analysis. The sequences were aligned by MUSCLE, and phylogenetic trees were built using MEGA-X software based on the nucleotide and translated AA sequences. RESULTS 98 isolates of complete N protein genes from ASEAN countries were analyzed. The nucleotides of all isolates were 97.5% conserved. Of 31 nucleotide changes, 22 led to amino acid (AA) substitutions; thus, the AA sequences were 94.5% conserved. The phylogenetic tree of nucleotide and AA sequences shows similar branches. Nucleotide variations in clade O (C28311T); clade GR (28881–28883 GGG>AAC); and clade GRY (28881–28883 GGG>AAC and C28977T) lead to specific branches corresponding to the clade within both trees. CONCLUSIONS The N protein sequences of SARS-CoV-2 across ASEAN countries are highly conserved. Most isolates were closely related to the reference sequence originating from China, except the isolates representing clade O, GR, and GRY which formed specific branches in the phylogenetic tree.

Molecular analysis of occult hepatitis B infection among Iranian HIV-positive patients

Aim: The aims of this study were to find out the prevalence of occult hepatitis B infection (OBI) in HIV-1 patients, as well as to analyze the mutational patterns of OBI-positive individuals. Materials & methods: 172 HBsAg-negative, HIV-1-positive patients were selected according to data extracted from questionnaires. HBV serologic and molecular assays were performed. An extensive mutational analysis was applied using direct sequencing on HBsAg. Results: Thirty-one samples (18%) were OBI positive. Among 24 available OBI-positive samples, 17 (71%) contained at least one mutation only within ‘a’ determinant region of HBsAg. A stretch of mutations was found between amino acid positions 121 and 136. The physicochemical properties of individual amino acid substitutions and their potential impacts on 3D structure of ‘a’ determinant mutants were also determined. Conclusion: HBV serologic assays are not reliable markers to exclude occult HBV infection in HIV-positive patients.

Efficient construction of a highly useful phage-displayed human antibody repertoire

We have constructed a highly useful phage-displayed human antibody repertoire with limited cloning efforts. Our strategy was to maximize diversity during the first steps of library construction through the use of various lymphoid sources from several donors, inclusion of different immunoglobulin isotypes, and performance of multiple separate amplification reactions with all possible combinations within a complex primer set. The resulting variable region collections were cloned to form a moderate size library, composed by 4.25x10(8) single chain antibody fragments. This repertoire was successfully used to retrieve binders to seven model antigens: six proteins and one 12 aa peptide. Binding affinities reached nanomolar and even subnanomolar range. Sequence diversity and V-gene usage variability among binders were proven. Our approach was not focused on absolute library size, but on a high quality sampling of variable regions from the human antibody repertoire.