During the current pandemic of COVID-19, the authors observed that during screening test for SARS-CoV-2 targeting the E-gene by qRT-PCR, few nasopharyngeal/oropharyngeal samples showed amplification signals at late cycle threshold (CT-value) > 35 despite being negative for other confirmatory target genes . Thirty such samples (taken as cases) showing detectable CT of> 35 cycle in E-gene which were negative for other target genes of SARS-CoV-2 and 30 samples with undetectable fluorescence in E-gene were taken as controls for investigation . An in-vitro diagnostic approved commercial qRT-PCR multiplex kit detecting 33 respiratory pathogens which can also detect Haemophilus influenzae was used for screening the samples . It was observed that out of the 30 samples showing detectable CT> 35 in E-gene , 11 samples were positive for Haemophilus influenzae whereas in the controls only three samples were positive for H. influenzae (p-value : 0.03) which was statistically significant . Further, the probes and primers were screened against H. influenzae for matches in the genome . It was observed that all primers and probes for the E-gene of SARS-CoV-2 had over 13 bp long sequences matching 100% with multiple sites across the H. influenzae genome . This qRT-PCR primer & probes are being used extensively across India, and laboratories using them should be aware of the cross-reactivity of primers & probes with the H. influenzae genome . Further, the authors observed that 95.9% (5415/5642) of COVID-19 positive cases detected in their laboratory were asymptomatic at the time of collection of samples . This warrants further investigations.