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Mehta, Priyanka; Sahni, Shweta; Siddiqui, Samreen; Mishra, Neha; Sharma, Pooja; Sharma, Sachin; Tyagi, Akansha; Chattopadhyay, Partha; Vivekanand, A; Devi, Priti; Khan, Azka; Waghdhare, Swati; Budhiraja, Sandeep; Uppili, Bharathram; Maurya, Ranjeet; Nangia, Vivek; Shamim, Uzma; Hazarika, Pranjal P.; Wadhwa, Saruchi; Tyagi, Nishu; Dewan, Arun; Tarai, Bansidhar; Das, Poonam; Faruq, Mohammed; Agrawal, Anurag; Jha, Sujeet; Pandey, Rajesh
Frontiers in microbiology, 05/2021, Letnik: 12Journal Article
Co-infection with ancillary pathogens is a significant modulator of morbidity and mortality in infectious diseases. There have been limited reports of co-infections accompanying SARS-CoV-2 infections, albeit lacking India specific study. The present study has made an effort toward elucidating the prevalence, diversity and characterization of co-infecting respiratory pathogens in the nasopharyngeal tract of SARS-CoV-2 positive patients. Two complementary metagenomics based sequencing approaches, Respiratory Virus Oligo Panel (RVOP) and Holo-seq, were utilized for unbiased detection of co-infecting viruses and bacteria. The limited SARS-CoV-2 clade diversity along with differential clinical phenotype seems to be partially explained by the observed spectrum of co-infections. We found a total of 43 bacteria and 29 viruses amongst the patients, with 18 viruses commonly captured by both the approaches. In addition to SARS-CoV-2, Human Mastadenovirus, known to cause respiratory distress, was present in a majority of the samples. We also found significant differences of bacterial reads based on clinical phenotype. Of all the bacterial species identified, ∼60% have been known to be involved in respiratory distress. Among the co-pathogens present in our sample cohort, anaerobic bacteria accounted for a preponderance of bacterial diversity with possible role in respiratory distress. Clostridium botulinum , Bacillus cereus and Halomonas sp. are anaerobes found abundantly across the samples. Our findings highlight the significance of metagenomics based diagnosis and detection of SARS-CoV-2 and other respiratory co-infections in the current pandemic to enable efficient treatment administration and better clinical management. To our knowledge this is the first study from India with a focus on the role of co-infections in SARS-CoV-2 clinical sub-phenotype.
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JCR | SNIP | JCR | SNIP | JCR | SNIP | JCR | SNIP |
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in: SICRIS
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