scholarly journals SARS-CoV-2 blood RNA load predicts outcome in critically ill COVID-19 patients

2021 ◽  
Author(s):  
Fabian Heinrich ◽  
Michael F Nentwich ◽  
Eric Bibiza-Freiwald ◽  
Dominik Nörz ◽  
Kevin Roedl ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Critically Ill ◽  
Viral Rna ◽  
Outcome Predictor ◽  
Treatment Allocation ◽  
Virus Clearance ◽  
Rna Quantification ◽  
Specimen Collection ◽  
Probability Of Death ◽  
Time Of Admission

Abstract: Background SARS-CoV-2 RNA loads in patient specimens may act as a clinical outcome predictor in critically ill patients with COVID-19. Methods We evaluated the predictive value of viral RNA loads and courses in the blood compared to the upper and lower respiratory tract loads of critically ill COVID-19 patients. Daily specimen collection and viral RNA quantification by RT-qPCR was performed in all consecutive 170 COVID-19 patients between March 2020 and February 2021 during the entire ICU stay (4145 samples analyzed). Patients were grouped according to their 90-days outcome as survivors (n=100) or non-survivors (n=70). Results In non-survivors, blood SARS-CoV-2 RNA loads were significantly higher at the time of admission to the ICU (p=0.0009). Failure of blood RNA clearance was observed in 33/50 (66 %) of the non-survivors compared to 12/64 (19 %) of survivors (p<0.0001). As determined by multivariate analysis, taking sociodemographic and clinical parameters into account, blood SARS-CoV-2 RNA load represents a valid and independent predictor of outcome in critically ill COVID-19 patients (OR [log10]: 0.23 [0.12 – 0.42], p<0.0001) with a significantly higher effect for survival compared to the respiratory tract SARS-CoV-2 RNA loads (OR [log10]: 0.75 [0.66 – 0.85], p<0.0001). Blood RNA loads exceeding 2.51 x 10 3 SARS-CoV-2 RNA copies/ml were found to indicate a 50% probability of death. Consistently, 29/33 (88%) of the non-survivors with failure of virus clearance exceeded this cut-off value constantly. Conclusion Blood SARS-CoV-2 load is an important independent outcome predictor and should be further evaluated for treatment allocation and patient monitoring.

scholarly journals The lower respiratory tract microbiome of critically ill patients with COVID-19

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Paolo Gaibani ◽  
Elisa Viciani ◽  
Michele Bartoletti ◽  
Russell E. Lewis ◽  
Tommaso Tonetti ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Critically Ill ◽  
Critically Ill Patients ◽  
Lower Respiratory Tract ◽  
Multidrug Resistant ◽  
Carbapenem Resistant ◽  
Lung Microbiome ◽  
Bacterial Microbiome ◽  
Unweighted Unifrac ◽  
Bacterial Superinfection

AbstractCOVID-19 infection may predispose to secondary bacterial infection which is associated with poor clinical outcome especially among critically ill patients. We aimed to characterize the lower respiratory tract bacterial microbiome of COVID-19 critically ill patients in comparison to COVID-19-negative patients. We performed a 16S rRNA profiling on bronchoalveolar lavage (BAL) samples collected between April and May 2020 from 24 COVID-19 critically ill subjects and 24 patients with non-COVID-19 pneumonia. Lung microbiome of critically ill patients with COVID-19 was characterized by a different bacterial diversity (PERMANOVA on weighted and unweighted UniFrac Pr(> F) = 0.001) compared to COVID-19-negative patients with pneumonia. Pseudomonas alcaligenes, Clostridium hiranonis, Acinetobacter schindleri, Sphingobacterium spp., Acinetobacter spp. and Enterobacteriaceae, characterized lung microbiome of COVID-19 critically ill patients (LDA score > 2), while COVID-19-negative patients showed a higher abundance of lung commensal bacteria (Haemophilus influenzae, Veillonella dispar, Granulicatella spp., Porphyromonas spp., and Streptococcus spp.). The incidence rate (IR) of infections during COVID-19 pandemic showed a significant increase of carbapenem-resistant Acinetobacter baumannii (CR-Ab) infection. In conclusion, SARS-CoV-2 infection and antibiotic pressure may predispose critically ill patients to bacterial superinfection due to opportunistic multidrug resistant pathogens.

Clinical correlates of herpes simplex virus type 1 loads in the lower respiratory tract of critically ill patients

2013 ◽  
Vol 58 (1) ◽  
pp. 79-83 ◽  
Author(s):  
Evelien Assink-de Jong ◽  
A.B. Johan Groeneveld ◽  
Annika M. Pettersson ◽  
Alex Koek ◽  
Christina M.J.E. Vandenbroucke-Grauls ◽  
...  
Keyword(s):  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Respiratory Tract ◽  
Critically Ill ◽  
Herpes Simplex Virus Type ◽  
Critically Ill Patients ◽  
Lower Respiratory Tract ◽  
Clinical Correlates ◽  
Simplex Virus

scholarly journals An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms

2021 ◽  
Author(s):  
Chrissy Eckstrand ◽  
Tom Baldwin ◽  
Mia Kim Torchetti ◽  
Mary Lea Killian ◽  
Kerry A Rood ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Clinical Signs ◽  
Viral Transmission ◽  
Viral Rna ◽  
Upper Respiratory Tract ◽  
Tracheobronchial Lymph Node ◽  
Multiple Organs ◽  
Upper Respiratory ◽  
Polymerase Chain

The breadth of animal hosts that are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and may serve as reservoirs for continued viral transmission are not known entirely. In August 2020, an outbreak of SARS-CoV-2 occurred in multiple mink farms in Utah and was associated with high mink mortality and rapid viral transmission between animals. The outbreak's epidemiology, pathology, molecular characterization, and tissue distribution of virus within infected mink is provided. Infection of mink was likely by reverse zoonosis. Once established, infection spread rapidly between independently housed animals and farms, and caused severe respiratory disease and death. Clinical signs were most notably sudden death, anorexia, and increased respiratory effort. Gross pathology examination revealed severe pulmonary congestion and edema. Microscopically there was pulmonary edema with moderate vasculitis, perivasculitis, and fibrinous interstitial pneumonia. Reverse transcriptase polymerase chain reaction (RT-PCR) of tissues collected at necropsy demonstrated the presence of SARS-CoV-2 viral RNA in multiple organs including nasal turbinates, lung, tracheobronchial lymph node, epithelial surfaces, and others. Whole genome sequencing from multiple mink was consistent with published SARS-CoV-2 genomes with few polymorphisms. The Utah mink SARS-CoV-2 strain fell into Clade GH, which is unique among mink and other animal strains sequenced to date and did not share other spike RBD mutations Y453F and F486L found in mink. Localization of viral RNA by in situ hybridization revealed a more localized infection, particularly of the upper respiratory tract. Mink in the outbreak reported herein had high levels of virus in the upper respiratory tract associated with mink-to-mink transmission in a confined housing environment and were particularly susceptible to disease and death due to SARS-CoV-2 infection.

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