ABSTRACT
Background. Lung reactivations of Herpesviridae, herpes simplex virus (HSV) and cytomegalovirus (CMV) have been reported in Covid-19 patients. Whether or not those viral reactivations are more frequent than in other patients is not known. Methods. Retrospective monocentric cohort study of 145 patients with severe Covid-19 pneumonia requiring invasive mechanical ventilation and who were tested for HSV and CMV in bronchoalveolar lavage performed during fiberoptic bronchoscopy for ventilator-associated pneumonia suspicion. Rates of HSV and CMV lung reactivations, and HSV bronchopneumonitis were assessed and compared with an historical cohort of 89 patients with severe influenza pneumonia requiring invasive mechanical ventilation. Results. Among the 145 Covid-19 patients included, 50% and 42 % had HSV and CMV lung reactivations, respectively;whereas among the 89 influenza patients, 63% and 28% had CMV lung reactivations, respectively. Cumulative incidence of HSV lung reactivation (taking into account extubation and death as competing events) was higher in influenza than in Covid-19 patients (p = 0.03, see figure 1), whereas the rate of HSV bronchopneumonitis was similar in both groups (31% and 25%, respectively). Cumulative incidence of CMV lung reactivation (taking into account extubation and death as competing events) was similar in Covid-19 and influenza patients (p=0.07). Outcomes of patients with HSV or CMV lung reactivations were similar to that of patients without, whatever the underlying conditions, i.e., in Covid-19 patients, in influenza patients, or when all patients were grouped. Estimated cumulative incidence of herpes simplex virus (HSV) lung reactivation, extubation or death in Covid-19 and influenza patients, taking into account only the first event that occurred. p values for differences between Covid-19 and influenza patients were 0.03 for HSV reactivation, 0.53 for death and 0.87 for extubation. Conclusion. HSV andCMVlung reactivations are frequent in Covid-19 patients, but not more frequent than in patients with influenza-associated severe pneumonia, despite a higher severity of illness at intensive care unit (ICU) admission of the latter and a longer duration of mechanical ventilation of the former. Although no impact on outcome of HSV and CMV lung reactivations was detected, the effect of antiviral treatment against these Herpesviridae remains to be determined in these patients. (Figure Presented).
ABSTRACT
France was one of the first countries to be reached by the COVID-19 pandemic. Here, we analyse 196 SARS-Cov-2 genomes collected between Jan 24 and Mar 24 2020, and perform a phylodynamics analysis. In particular, we analyse the doubling time, reproduction number (Rt) and infection duration associated with the epidemic wave that was detected in incidence data starting from Feb 27. Different models suggest a slowing down of the epidemic in Mar, which would be consistent with the implementation of the national lock-down on Mar 17. The inferred distributions for the effective infection duration and Rt are in line with those estimated from contact tracing data. Finally, based on the available sequence data, we estimate that the French epidemic wave originated between mid-Jan and early Feb. Overall, this analysis shows the potential to use sequence genomic data to inform public health decisions in an epidemic crisis context and calls for further analyses with denser sampling.
ABSTRACT
Background: Data on incidence, clinical presentation and outcomes of ventilator-associated pneumonia (VAP) in patients with severe coronavirus disease 2019 (COVID-19) pneumonia requiring mechanical ventilation (MV) are limited. Methods: Case series of patients with COVID-19 pneumonia admitted to a single ICU in France. All consecutive patients requiring MV with RT-PCR-confirmed SARS-CoV-2 infection between March 12th and April 24th, 2020 were included. Frequency, clinical characteristics, responsible pathogens and outcomes of VAP were assessed, and compared to an historical cohort of patients with severe influenza-associated pneumonia requiring MV admitted to the same ICU during the preceding three winter seasons. Results: Fifty-four consecutive patients with COVID-19-associated respiratory failure requiring MV were included (median (IQR) age 48 (42-58) years;74% male;93% requiring veno-venous ECMO). VAP occurred in 46 (85%) of them (median (IQR) prior MV duration before the first episode, 11 (8-16) days) (Table 1). Pathogens responsible for VAP were predominantly Enterobacteriaceae (72%), and particularly inducible AmpC-cephalosporinase producers (41%), followed by Pseudomonas aeruginosa (35%) (Table 2). Pulmonary infection recurrence and death were observed in 46 (85%) and 17 (31%) patients, respectively. Details on recurrent episodes and pathogens responsible for recurrences are given in Table 3. Most recurrences were relapse (i.e. infection with the same pathogen), with a high proportion occurring during antimicrobial treatment despite its adequacy. Despite a high rate of P. aeruginosa VAP in patients with influenza-associated ARDS, pulmonary infection recurrence rate was significantly lower than in patients with COVID-19. Overall mortality was similar in the two groups. Baseline characteristics of patientsConclusion: Patients with severe COVID-19-associated respiratory failure requiring MV had a very high late-onset VAP rate. Inducible AmpC cephalosporinase- producing Enterobacteriaceae and Pseudomonas aeruginosa appeared to be frequently responsible for VAP, with multiple subsequent episodes and difficulties to eradicate the pathogen from the lung.
ABSTRACT
Introduction Au 30 avril 2020, plus de 3 millions de personnes dans le monde étaient infectées par le coronavirus responsable du syndrome respiratoire aigu sévère 2 (SARS-CoV-2), dont environ 130 000 en France. Le nombre croissant de patients sur une durée courte a surchargé les structures hospitalières tant en ambulatoire (SAU) qu’en hospitalisation ou en réanimation. L’acide ribonucléique (ARN) du SARS-CoV-2 peut être détecté dans de nombreux sites anatomiques et liquides biologiques. Les prélèvements nasopharyngés (NP) sont les plus utilisés à des fins de diagnostic. La charge virale (CV) peut être estimée par le nombre de cycle de RT-PCR nécessaire pour obtenir un signal détectable. Les liens entre le niveau de CV sur un prélèvement NP et la gravité clinique, la progression et la transmission de la maladie sont insuffisamment connus. Nous avons mené une étude de cohorte rétrospective monocentrique afin d’évaluer les liens entre la CV et l’évolution de la maladie liée SARS-CoV-2 lors des quatre premiers mois de l’épidémie en France métropolitaine. Matériels et méthodes Étude rétrospective descriptive chez les adultes admis du 25 janvier au 30 avril 2020 dans un service des maladies infectieuses pour une infection SARS-CoV-2 biologiquement confirmée. Les données épidémiologiques, cliniques, biologiques et thérapeutiques ont été saisies à partir des dossiers médicaux informatisés. La charge virale ARN a été estimée dans les échantillons NP à partir des valeurs du nombre de cycle de RT-PCR nécessaire pour obtenir un signal détectable (CT) selon trois techniques successives, détectant toutes sur le gène E. du SARS-CoV-2. Une CV haute correspondait à un nombre de CT bas. Résultats Du 01/03 au 30/04/2020, 159 patients ont eu une estimation de la CV NP à l’admission : 84 hommes et 75 femmes, d’âge médian de 66 ans [28–10]. L’évolution a été défavorable pour 29 (18,2 %) patients. Dix-sept (10,7 %) ont été transférés en soins intensifs, 12 (7,5 %) patients tous âgés. Quatre-vingt-quinze patients ont pu bénéficier d’une estimation de la CV fiable. Le CT médian était de 31,49 cycles [17,84–38,88]. Il n’existait pas de différence significative de la CV NP initiale en termes de sexe ou d’âge. Toutefois une tendance d’augmentation avec l’âge existait. Sur une analyse en sous-groupe sur 46 patients ayant eu un par PCR NP une baisse de la CV a été observé au cours de l’hospitalisation. La CV NP initiale était plus élevée chez les patients décédés par rapport aux patients transférés en réanimation survivants et aux patients survivants non transférés en réanimation (CT=25,9, 30,7 et 31,5). Aucun des 29 (18,2 %) patients avec une CV faible (CT ≥ 34) n’est décédé. Conclusion La valeur du CT de RT-PCR mesurée par une technique standardisée permet d’estimée la CV des patients sur les prélèvements NP. Une CV basse semble associé à un meilleur pronostic. L’estimation de la CV nécessite d’être étudiée sur un plus grand échantillon afin d’étudier son potentiel intérêt pronostique dans l’évaluation initiale des patients.