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Major oncogenic determinants, including CagA, VacA, and the type IV secretion system, show marked geographic heterogeneity, yet the evolutionary forces shaping this uneven distribution remain unclear. Prophages can mediate horizontal gene transfer and modulate bacterial fitness and virulence, but their contribution to\n                      <jats:styled-content style=\"fixed-case\">\n                        <jats:italic>H. pylori<\/jats:italic>\n                      <\/jats:styled-content>\n                      carcinogenicity has not been systematically evaluated.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We characterized prophage diversity, population structure, and virulence potential using 2379\n                      <jats:styled-content style=\"fixed-case\">\n                        <jats:italic>H. pylori<\/jats:italic>\n                      <\/jats:styled-content>\n                      host genomes and 139 complete prophage genomes. Prophage population structure and intergenomic relatedness were inferred, and the prophage pangenome and protein\u2010sharing network were reconstructed. Homology\u2010based association analyses were performed to test enrichment of prophage orthologous groups (POGs) with major oncogenic virulence factors (CagA and\/or VacA) across the 2379 host genomes.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Prophages segregated into geographically structured populations. The EastAsia and EastAsia2 prophage groups were tightly coupled to high\u2010risk hspEAsia hosts and exhibited the largest and most diverse accessory repertoires. Virulence\u2010associated genes were strongly population\u2010specific and were detected only in the EastAsia\/EastAsia2 prophage populations. Moreover, carriage of POGs homologs from 1961P, HPy1R, and phiHP33 showed significant positive associations with CagA and\/or VacA across the 2379 genomes, whereas no enrichment was observed for KHP30 or KHP40.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      <jats:styled-content style=\"fixed-case\">\n                        <jats:italic>H. pylori<\/jats:italic>\n                      <\/jats:styled-content>\n                      prophages are not passive genomic remnants but population\u2010structured reservoirs whose gene repertoires track high\u2010risk virulence backgrounds and may contribute to the bacterium's carcinogenic potential.\n                    <\/jats:p>\n                  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