Respiratory Co-Infections: Modulators of SARS-CoV-2 Patients’ Clinical Sub-Phenotype

• DOI: 10.3389/fmicb.2021.653399
• Publication Date: 2021-05-28T07:53:55Z
• Authors: Priyanka Mehta; Shweta Sahni; Samreen Siddiqui; Neha Mishra; Pooja Sharma; Sachin Sharma; Akansha Tyagi; Partha Chattopadhyay; A Vivekanand; Priti Devi; Azka Khan; Swati Waghdhare; Sandeep Budhiraja; Bharathram Uppili; Ranjeet Maurya; Vivek Nangia; Uzma Shamim; Pranjal P. Hazarika; Saruchi Wadhwa; Nishu Tyagi; Arun Dewan; Bansidhar Tarai; Poonam Das; Mohammed Faruq; Anurag Agrawal; Sujeet Jha; Rajesh Pandey
• Keywords: Epidemiology; Immunology; Respiratory tract infections; Microbiology; Respiratory system; Gene; 03 medical and health sciences; co-infection; respiratory viruses; Biochemistry, Genetics and Molecular Biology; Virology; RVOP; Health Sciences; Epidemiology and Pathogenesis of Respiratory Viral Infections; Genetics; holotranscriptome; Molecular Biology; Biology; metagenomics; 0303 health sciences; Ecology; Obesity-associated Microbiome; FOS: Clinical medicine; COVID-19; Life Sciences; Diversity and Function of Gut Microbiome; Ecology and Evolution of Viruses in Ecosystems; QR1-502; 3. Good health; FOS: Biological sciences; Environmental Science; Physical Sciences; Medicine; Metagenomics; Anatomy

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.