Fatal Pneumonia Associated With a Novel Genotype of Human Coronavirus OC43

Since its first discovery in 1967, human coronavirus OC43 (HCoV-OC43) has been associated with mild self-limiting upper respiratory infections worldwide. Fatal primary pneumonia due to HCoV-OC43 is not frequently described. This study describes a case of fatal primary pneumonia associated with HCoV-OC43 in a 75-year-old patient with good past health. The viral loads of the respiratory tract specimens (bronchoalveolar lavage and endotracheal aspirate) from diagnosis to death were persistently high (3.49 × 106–1.10 × 1010 copies/ml). HCoV-OC43 at a 6.46 × 103 copies/ml level was also detected from his pleural fluid 2 days before his death. Complete genome sequencing and phylogenetic analysis showed that the present HCoV-OC43 forms a distinct cluster with three other HCoV-OC43 from United States, with a bootstrap value of 100% and sharing 99.9% nucleotide identities. Pairwise genetic distance between this cluster and other HCoV-OC43 genotypes ranged from 0.27 ± 0.02% to 1.25 ± 0.01%. In contrast, the lowest pairwise genetic distance between existing HCoV-OC43 genotypes was 0.26 ± 0.02%, suggesting that this cluster constitutes a novel HCoV-OC43 genotype, which we named genotype I. Unlike genotypes D, E, F, G, and H, no recombination event was observed for this novel genotype. Structural modeling revealed that the loop with the S1/S2 cleavage site was four amino acids longer than other HCoV-OC43, making it more exposed and accessible to protease, which may have resulted in its possible hypervirulence.

Bacteriological profile and their antibiogram from Endotracheal aspirate and Bronchoalveolar lavage fluid samples from intensive care unit patients

Bacterial respiratory infections are most commonly causes of illness for all age group patients in ICU. Most of the patients suffer from urosepsis, postoperative disease and lower respiratory infection when admitted in ICU’s. The main purpose of this study is control in ICU’s infection & determine their antibiotic sensitivity pattern for better treatment of patients. Bacteriological profile and their antibiogram from endotracheal aspirate and bronchoalveolar lavage fluid samples from intensive care unit patients.We performed manual culture of Endotracheal aspirate & BAL fluid specimens collected from ICU’s patients. Samples were cultured on Blood agar and Mac-Conkey agar then incubated at 37C for 24 hours. Any growth were further confirmed by Gram stain and appropriate biochemical tests, and then Antibiotic sensitivity test was done. Among the 123 mechanically ventilated patients and 68 of them developed positive samples. In this study 55.3% (68) pathogenic isolates, 4.1% (5) were non pathogenic isolates and 40.6 (50) were no growth isolates in BAL and endotracheal aspirate samples. In which 67.6% (46) male and 32.4% (22) female patients. Older population falling in the 40-50 years of age group contributes the majority (27.64%) of the infection undergoing treatment for LRT infection in ICU’s patients in TMMC & RC, Moradabad, and in 70-80 years of age group (4.06%) was less contributes of this infection. Among the causative agents, were most common among gram negatives and was common among the gram positive isolates. In our study more resistance gram positive antibiotics were CIP, E, LE, and most sensitive antibiotics were VA, LZ, GEN and TEI. And gram negative bacteria most resistant antibiotics were OF, CPM, CAZ, CIP, CTR, MRP, LE, IPM, PIT and most sensitive antibiotics were AK, GEN, CL, TGC. In this study we conclude that Gram-negative bacilli were predominant in BAL fluid and endotracheal aspirates of ICU patients. Out of 68 multidrug resistance isolates, 1.47% were MRSA, 41.17% were ESBL and 57.36% were MBL isolates higher rate of ESBL production seen in spp., and higher rate of MBL production in spp.High incidence of VAP and the potential MDR pathogens are a real threat in our ICU’s. Combined approach of judicious antibiotic usage and training programs to health care personnel might be of help in combatting high incidence of antibiotic resistance in our institute.

Immune responses in COVID-19 respiratory tract and blood reveal mechanisms of disease severity

Although the respiratory tract is the primary site of SARS-CoV-2 infection and the ensuing immunopathology, respiratory immune responses are understudied and urgently needed to understand mechanisms underlying COVID-19 disease pathogenesis. We collected paired longitudinal blood and respiratory tract samples (endotracheal aspirate, sputum or pleural fluid) from hospitalized COVID-19 patients and non-COVID-19 controls. Cellular, humoral and cytokine responses were analysed and correlated with clinical data. SARS-CoV-2-specific IgM, IgG and IgA antibodies were detected using ELISA and multiplex assay in both the respiratory tract and blood of COVID-19 patients, although a higher receptor binding domain (RBD)-specific IgM and IgG seroconversion level was found in respiratory specimens. SARS-CoV-2 neutralization activity in respiratory samples was detected only when high levels of RBD-specific antibodies were present. Strikingly, cytokine/chemokine levels and profiles greatly differed between respiratory samples and plasma, indicating that inflammation needs to be assessed in respiratory specimens for the accurate assessment of SARS-CoV-2 immunopathology. Diverse immune cell subsets were detected in respiratory samples, albeit dominated by neutrophils. Importantly, we also showed that dexamethasone and/or remdesivir treatment did not affect humoral responses in blood of COVID-19 patients. Overall, our study unveils stark differences in innate and adaptive immune responses between respiratory samples and blood and provides important insights into effect of drug therapy on immune responses in COVID-19 patients.

Immune responses in COVID-19 respiratory tract and blood reveal mechanisms of disease severity

Although the respiratory tract is the primary site of SARS-CoV-2 infection and the ensuing immunopathology, respiratory immune responses are understudied and urgently needed to understand mechanisms underlying COVID-19 disease pathogenesis. We collected paired longitudinal blood and respiratory tract samples (endotracheal aspirate, sputum or pleural fluid) from hospitalized COVID-19 patients and non-COVID-19 controls. Cellular, humoral and cytokine responses were analysed and correlated with clinical data. SARS-CoV-2-specific IgM, IgG and IgA antibodies were detected using ELISA and multiplex assay in both the respiratory tract and blood of COVID-19 patients, although a higher receptor binding domain (RBD)-specific IgM and IgG seroconversion level was found in respiratory specimens. SARS-CoV-2 neutralization activity in respiratory samples was detected only when high levels of RBD-specific antibodies were present. Strikingly, cytokine/chemokine levels and profiles greatly differed between respiratory samples and plasma, indicating that inflammation needs to be assessed in respiratory specimens for the accurate assessment of SARS-CoV-2 immunopathology. Diverse immune cell subsets were detected in respiratory samples, albeit dominated by neutrophils. Importantly, we also showed that dexamethasone and/or remdesivir treatment did not affect humoral responses in blood of COVID-19 patients. Overall, our study unveils stark differences in innate and adaptive immune responses between respiratory samples and blood and provides important insights into effect of drug therapy on immune responses in COVID-19 patients.

Spectrum of Bacterial Co-Infections of the Lower Respiratory Tract in COVID 19 Patients Admitted to the ICU of a Tertiary Care Hospital

Aims: We aimed to evaluate the burden of bacterial co-infections in patients with COVID-19 and to ensure judicious use of antibiotics. Study Design: Hospital based, cross sectional study. Place and Duration of Study: Postgraduate department of Microbiology, Government Medical College, Srinagar, and associated hospitals, between July 2020 and February 2021. Methodology: A total of 70 patients diagnosed with COVID-19 by RT PCR of nasopharyngeal/oropharyngeal samples were included in the study. Lower respiratory specimen like endotracheal aspirate (ETA), sputum, and bronchoalveolar lavage (BAL) from COVID-19 patients admitted in the ICU were collected as per standard protocol and subjected to quantitative cultures in the laboratory. Antimicrobial susceptibility testing was carried out in line with CLSI recommendations. Results: Of the 70 lower respiratory tract specimens (Endotracheal aspirate n=53, sputum n=15, and Bronchoalveolar lavage n=02) taken from RT-PCR confirmed COVID-19 patients, 51 (72.9%) showed microbiological evidence of bacterial infection by culture positivity. 28/51 (55%) were males and 23/51 (45%) were females, mean age was 54 years (range= 16-85 years). Majority of the organisms recovered (n=51, 83%) were Gram-negative bacilli, among which Acinetobacter spp. (n=27, 53%) followed by Klebsiella pneumoniae (n=06, 12%) were the most common. Among Gram positive organisms, methicillin resistant Staphylococcus aureus and Enterococcus sp were most commonly isolated. Conclusion: It is evident from our study that superinfection in COVID-19 patients due to Acinetobacter baumannii and Staphylococcus aureus is of serious concern. Timely treatment of these infections is pivotal to decrease the morbidity and mortality rates in COVID-19-infected patients.