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

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.

COVID-19 and spinal cord injury and disease: results of an international survey as the pandemic progresses.

STUDY DESIGN: An online survey. OBJECTIVES: To follow-up with and re-query the international spinal cord community's response to the Coronavirus Disease 2019 (COVID-19) pandemic by revisiting questions posed in a previous survey and investigating new lines of inquiry. SETTING: An international collaboration of authors and participants. METHODS: Two identical surveys (one in English and one in Spanish) were distributed via the internet. Responses from both surveys were pooled and analyzed for demographic and response data. RESULTS: Three hundred and sixty-six respondents were gathered from multiple continents and regions. The majority (63.1%) were rehabilitation physicians and only 12.1% had patients with spinal cord injury/disease (SCI/D) that they knew had COVID-19. Participants reported that the COVID-19 pandemic had caused limited access to clinician and support services and worsening medical complications. Nearly 40% of inpatient clinicians reported that "some or all" of their facilities' beds were being used by medical and surgical patients, rather than by individuals requiring inpatient rehabilitation. Respondents reported a 25.1% increase in use of telemedicine during the pandemic (35% used it before; 60.1% during), though over 60% felt the technology incompletely met their patients' needs. CONCLUSION: The COVID-19 pandemic has negatively impacted the ability of individuals with SCI/D to obtain their "usual level of care." Moving forward into a potential "second wave" of COVID-19, patient advocacy and efforts to secure access to thorough and accessible care are essential.

Integrated genomic view of SARS-CoV-2 in India.

Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.