Arginine Residues in Antiviral Ab Are Often Created by SHM of AGY Ser Codons
An abundance of CDR codons that are prone to mutate to encode antinuclear Ab seemed paradoxical. However, there is speculation that a modest degree of autoreactivity may be beneficial to antiviral immune responses (37–39). For example, some viruses display host-derived nuclear material on their capsids that might enhance B cell activation or antibody efficacy due to an avidity effect (40). Therefore, we sought to determine if Arg residues are frequently generated via SHM in antiviral Ab. At first, we examined somatic mutations in broadly neutralizing antibodies (bNAbs) against HIV. Although we found that somatic mutations in AGY codons frequently produced Arg codons in these Abs, the results were not easily interpreted because overall mutation frequencies were extremely high, and in many cases CDR boundaries could not be defined due to insertions and deletions. Therefore, we extended our analysis to 298 published sequences of human antibodies against eight other virus species or subspecies. This analysis revealed frequent somatic mutations converting AGY Ser codons in CDRs to Arg codons.
In two human studies involving the H1N1 influenza virus (23, 24), 17 out of 46 and 24 out of 49 antibodies had at least one AGY Ser to Arg amino acid replacement resulting from SHM (Figure 3A). Arg replacement mutations in CDR sequences accounted for 2.9 and 3.1% of all V-region gene missense mutations (CDRs and FRs) in the two studies, with replacements at germline AGY codons comprising most of these (2 and 2.23%). A similar trend was observed in antibodies against hepatitis A, B, and C, rhino, dengue, avian influenza, and West Nile viruses. CDR Arg mutations accounted for 2.4–9.4% of all missense mutations in V-region genes for these antibodies, most of which (1.5–6.6%) occurred at germline CDR AGY codons (Figure 3B; Table 1).
Figure 3  Somatically generated Arg codons often arise at germline CDR AGY Ser codons in antiviral immune responses. (A) Sequences and analyses from two studies of anti-H1N1 antibodies, as described in Section “Materials and Methods.” Heavy and light chains for a particular clone were combined to generate data for the graphs. The data combine the results of CDR and FR analyses. Any → Arg indicates a mutation at any non-Arg codon that gives rise to an Arg codon. Ser → Arg indicates an AGY Ser codon to Arg codon mutation. Numbers inside graphs indicate number of clones that were analyzed (heavy plus light chain). (B) Bars represent the average number of indicated replacement mutations among antiviral antibodies (heavy or light chain genes). Influenza #1 (n = 92), Influenza #2 (n = 98), Rhinovirus (n = 12), Avian Influenza (n = 27), West Nile (n = 6), Dengue virus (n = 4), Hepatitis A, B and C (n = 59).
Table 1  Amino acid replacements via SHM of CDR AGY Ser codons.
Immunogen  Asn (%)  Gly (%)  Thr (%)  Arg (%)  Others (%)  #CDR AGY SHM
Influenzaa  22c  16c  19c  11  32  142
Influenzab  30c  12  23c  16  19  107
West Nile  20  0  60c  20  0  5
Dengue  14  0  43c  29  14  7
Rhinovirus  7  0  15  26  52  27
Avian Influenza  50c  0  17  33  0  12
Hep. A, B, and C  22c  18  18  20  22  72
aAntibody sequences from Wrammert et al. (23).
bAntibody sequences from Li et al. (24).
cAmino acid replacements that occurred more often than Arg replacements at CDR AGY Ser codons.