| Criteria | hpAfrica1 | hpAfrica2 | hpNEAfrica | Remarks |
| Geographic Origin | West and Central Africa | Southern Africa | Northeastern Africa (Horn of Africa, Egypt, Sudan) | Reflects distinct ancestral origins and human migration histories |
| Ancestral Components | Ancestry from AE1 (Ancestral Europe 1) and AE2 (Ancestral Africa) | Predominantly AE2 | Mix of AE2 and some influence from AE1 | hpNEAfrica shows admixture compared to more isolated hpAfrica2 |
| Phylogeographic Distribution | Present in African populations and African diaspora (e.g., Americas) | Restricted mainly to Khoisan and Bantu-speaking populations | Found in Nile Valley and surrounding regions | hpAfrica1 shows broad distribution; hpAfrica2 is most restricted geographically |
| Virulence Gene Profile | Often cagA-positive, vacA s1/m1 alleles | Frequently cagA-negative or non-functional cagPAI | Variable cagA, sometimes atypical EPIYA motifs | hpAfrica1 strains tend to be more virulent |
| Clinical Relevance | Associated with higher inflammation, possible increased risk of disease | Less associated with severe gastric disease | Clinical impact under investigation | hpAfrica1 may have stronger pathogenic potential; hpAfrica2 considered less virulent |
| Genetic Diversity | High | High, but more divergent from global strains | Intermediate | hpAfrica2 diverged early from other H. pylori lineages |
| Evolutionary Significance | Thought to have co-evolved with humans during out-of-Africa migration | Believed to represent an ancient lineage | Possibly a product of recombination between hpAfrica1 and hpAfrica2 | Important for tracing human evolution and bacterial adaptation |
| Genomic Features | Well-studied, several complete genomes available | Understudied, limited genome data | Moderate genomic data available | hpAfrica2 underrepresented in genomic surveillance |
| Host Adaptation | Well-adapted to various human hosts globally | Highly adapted to indigenous African groups | Adapted to populations in northeast Africa | Host–pathogen coevolution differs across lineages |
