Cross comparison of AmpFire HPV genotyping assay and Roche human papillomavirus (HPV) linear array for HPV genotyping of anal swab samples

•Overall agreement between AmpFire and Roche-LA was 89.9 % for anal specimens.•Highest concordance of 93.3 % was seen for HPV16.•AmpFire (90 min) has a faster turnaround time than Roche-LA (270 min).•High rate of anal infection with HR-HPV (90.6 %; AmpFire or 87.9 %; Roche-LA) in a population of HIV-infected MSM.•Multiple HR-HPV genotypes (75.2 %; AmpFire or 63.8 %; Roche-LA) were found in a population of HIV-infected MSM.