Cloning, sequencing, and polymorphism analysis of novel classical MHC class I alleles in northern pig-tailed macaques (Macaca leonina)

Abstract

The northern pig-tailed macaque (Macaca leonina) has been confirmed to be an independent species from the pig-tailed macaque group of Old World monkey. We have previously reported that the northern pig-tailed macaques were also susceptible to HIV-1. Here, to make this animal a potential HIV/AIDS model and to discover the mechanism of virus control, we attempted to assess the role of major histocompatibility complex (MHC) class I-restricted immune responses to HIV-1 infection, which was associated with viral replication and disease progression. As an initial step, we first cloned and characterized the classical MHC class I gene of northern pig-tailed macaques. In this study, we identified 39 MHC class I alleles including 17 MHC-A and 22 MHC-B alleles. Out of these identified alleles, 30 were novel and 9 were identical to alleles previously reported from other macaque species. The MHC-A and MHC-B loci were both duplicates as rhesus macaques and southern pig-tailed macaques. In addition, we also detected the patterns of positive selection in northern pig-tailed macaques and revealed the existence of balance selection with 20 positive selection sites in the peptide binding region. The analysis of B and F peptide binding pockets in northern and southern pig-tailed macaques and rhesus macaques suggested that they were likely to share a few common peptides to present. Thus, this study provides important MHC immunogenetics information and adds values to northern pig-tailed macaques as a promising HIV/AIDS model.

MHC class I allele diversity in cynomolgus macaques of Vietnamese origin

“…The diversity of nucleotide sequences encoding PBS or TBS ( Pi = 0.162) in the Mafa-A1 was predominantly higher than that in non-PBS or non-TBS coding regions ( Pi = 0.035) of the corresponding alleles (Table 3). This is consistent with the observation that high polymorphism at these functional residues is significant to increase the depth and breadth of the weaponry to cope with variant pathogens during evolution (Robinson et al, 2017; Lian et al, 2016). All of these 54 functional residues were listed in Fig.…”

Peer Review #3 of "MHC class I allele diversity in cynomolgus macaques of Vietnamese origin (v0.2)"

“…The diversity of nucleotide sequences encoding PBS or TBS (Pi=0.162) in the Mafa-A1 was predominantly higher than that in non-PBS or non-TBS coding regions (Pi=0.035) of the corresponding alleles (Table 3). This is consistent with the observation that high polymorphism at these functional residues is significant to increase the depth and breadth of the weaponry to cope with variant pathogens during evolution 2,67 . All of these 54 functional residues were listed in Figure 4 Manuscript to be reviewed…”

MHC class I diversity of olive baboons (Papio anubis) unravelled by next-generation sequencing

“…Long-range NGS on two different platforms, Roche 454 and PacBio SMRT, allowed the discovery of a high number of MHC class I A ( n = 21) and B alleles ( n = 80) in the olive baboon. For Paan-A and Paan-B alleles, different transcription levels have been observed, and it is a phenomenon known for other OWM species such as rhesus, cynomolgus, and pigtailed macaques (Fernandez et al 2011 ; Karl et al 2013 , 2017 ; Lian et al 2016 ; Otting et al 2005 , 2007 , 2009 , 2012 ). Additionally, the occurrence of different numbers of loci per haplotype—especially within the B region—is also comparable to the situation in macaques.…”