Purpose Influenza A viruses, human coronaviruses (hCoV) and human bocavirus (hBoV) are emerging res- piratory viruses. This study investigated the association between influenza A viruses co-infection with hBoV and hCoV and severity and the sensitivity of a real-time poly- merase chain reaction (RT-PCR) assay for identification of 15 coronaviruses. Methodology Published sequences for the 15 human coronaviruses were used to design a consensus PCR tar- geting the replicase open reading frame 1b. A previously published PCR targeting the NS1 Gene of all known human bocavirus strains was also utilized. A series of 217 samples from patients aged 37.7 (SD ± 30.4)] with sea- sonal influenza A viruses (SeasFluA) identified between 06/2011 and 06/2012 in NW England were tested for hCoV and hBoV using RT-PCR. Association between co- infection and disease outcome was assessed using logistic regression. Results The limit of detection of hCoV RT-PCR assay was 2 copies/μl of human coronavirus RNA template, a sensitivity comparable to a previously published SYBR green assay for human coronaviruses. A total of 12 hCoV and 17 hBoV were identified in the 217 influenza A posi- tive samples. A higher proportion (61.5 %; 8/13) of SeasFluA/hBoV co-infections were identified in patients that were admitted either to a general ward or the intensive care unit compared to 44.3 % (66/149) of single SeasFlu A virus infections (OR 2.5 95 % CI 0.67–9.34, p = 0.17). In a stratified analysis, there was a trend towards higher asso- ciation between FluA, hCoV and hBoV with increasing age (especially in patients aged 24–45 years and >65 year old). Conclusion Our hCoV RT-PCR protocol appeared to be of adequate analytical sensitivity for diagnosis. More and larger studies are needed to confirm the role of hCoV, hBoV in causing severe disease when they co-infect with influenza A viruses.