• Pourcentage de PCR SARS-Cov2 positif dans les syndromes grippaux: 5% dans les cas légers.

    Community Prevalence of #SARS-CoV-2 Among Patients With Influenzalike Illnesses Presenting to a Los Angeles Medical Center in March 2020 | Geriatrics | JAMA | JAMA Network
    https://jamanetwork.com/journals/jama/fullarticle/2764137

    (”These patients had sufficiently mild illness to be active in the community throughout their illness, increasing the possibility of #transmission.”)

    (PCR for influenza, respiratory syncytial virus and SARS-CoV-2)

    One hundred thirty-one tests for SARS-CoV-2 were obtained and 7 were positive ( 5.3% ; 95% CI, 2.2%-10.7%). The median age of patients who tested positive was 38 years (range, 34-44 years), 3 were male (43%), and the median duration of symptoms was 4 days (range, 2-4 days) at presentation. Six of 7 patients presented with fever, 5 with myalgias, and only 1 with cough. Only 1 patient had a travel history (returned from Miami, Florida). All patients had mild illnesses, and all tested negative for influenza and respiratory syncytial virus.

    #covid-19 #coronavirus #etats-unis

    • Dans les cas un peu plus sévères, 8%,

      Rapid Sentinel Surveillance for COVID-19 — Santa Clara County, California, March 2020 | MMWR
      https://www.cdc.gov/mmwr/volumes/69/wr/mm6914e3.htm

      Among 226 patients who met the inclusion criteria [patients with respiratory symptoms (e.g., fever, cough, or shortness of breath)], 23% had positive test results for influenza. Among patients who had negative test results for influenza, 79 specimens were tested for SARS-CoV-2, and 11% had evidence of infection.

      [...]

      If it is assumed there were no influenza and SARS-CoV-2 coinfections and that persons with negative test results for influenza and not tested for SARS-CoV-2 were similar to those who were tested, then an estimated 8% (19 of 226) of persons seen at participating urgent care centers with respiratory symptoms had COVID-19. This is similar to the 5% SARS-CoV-2 infection rate identified among patients evaluated for mild influenza-like illness at one Los Angeles medical center during a similar time frame (étude du JAMA).

  • Virological assessment of hospitalized patients with #COVID-2019 | Nature
    https://www.nature.com/articles/s41586-020-2196-x

    COVID modéré
    PCR et culture du virus dans différents milieux à différents temps :
    – Culture crachats se négative avant négativité PCR (cependant la charge virale diminue alors en-dessous d’un certain seuil)
    – culture toujours negative dans les selles malgré des PCR fortement positifs et la preuve d’une réplication active : du fait de la forme non sévère ou neutralisation du virus dans le tube digestif ?

    Conseil pratique pour désengorger les hôpitaux : sortie à domicile après le dixième jour avec un PCR en-dessous d’un certain seuil.

    To understand infectivity, live virus isolation was attempted on multiple occasions from clinical samples (Figure 1D). Whereas virus was readily isolatedً during the first week of symptoms from a considerable fraction of samples (16.66% in swabs, 83.33% in sputum samples), no isolates were obtained from samples taken after day 8 in spite of ongoing high viral loads . Virus isolation from stool samples was never successful, irrespective of viral RNA concentration, based on a total of 13 samples taken between days six to twelve from four patients. Virus isolation success also depended on viral load: samples containing < 10 [puissance 6] copies/mL (or copies per sample) never yielded an isolate.

    For swab and sputum, interpolation based on a probit model was done to obtain laboratory-based infectivity criteria for discharge of patients (Figures 1E, F). High viral loads and successful isolation from early throat swabs suggested potential virus replication in upper respiratory tract tissues.

    To obtain proof of active virus replication in absence of histopathology, we conducted RT-PCR tests to identify viral subgenomic messenger RNAs (sgRNA) directly in clinical samples (extended data Figure S1). Viral sgRNA is only transcribed in infected cells and is not packaged into virions, therefore indicating the presence of actively-infected cells in samples. Viral sgRNA was compared against viral genomic RNA in the same sample. In sputum samples taken on days 4/5, 6/7, and 8/9, a time in which active replication in sputum was obvious in all patients as per longitudinal viral load courses (see below), mean normalized sgRNA per genome ratios were ~0.4% (Figure 1G). A decline occurred over days 10/11. In throat swabs, samples taken up to day 5 were in the same range, while no sgRNA was detectable in swabs thereafter. Together, these data indicate active replication of SARS-CoV-2 in the throat during the first 5 days after symptoms onset. No, or only minimal, indication of replication in stool was obtained by the same method (Figure 1G).

    [...]

    The combination of very high virus RNA concentrations and occasional detection of sgRNA-containing cells in stool indicate active replication in the gastrointestinal tract. Our failure to isolate live #SARS-CoV-2 from stool may be due to the mild courses of cases, with only one case showing intermittent diarrhea. Further studies should therefore address whether SARS-CoV-2 shed in stool is rendered non-infectious though contact with the gut environment.

    Our initial results suggest that measures to contain viral spread should aim at droplet-, rather than fomite-based transmission.

    The prolonged viral shedding in sputum is relevant not only for hospital infection control, but also for discharge management. In a situation characterized by limited capacity of hospital beds in infectious diseases wards, there is pressure for early discharge following treatment. Based on the present findings, early discharge with ensuing home isolation could be chosen for patients who are beyond day 10 of symptoms with less than 100,000 viral RNA copies per ml of sputum. Both criteria predict that there is little residual risk of infectivity, based on cell culture.

    #PCR

  • Les courbes du 26 mars :

    – Le graphique du dessus représente le nombre de décès quotidiens (non cumulés, donc), cette fois en échelle linéaire, pour faire ressortir le fait que les évolutions pourraient bien commencer à s’éloigner de la progression exponentielle des débuts.

    – C’est l’évolution italienne qui a une rupture de plus en plus nette avec la progression exponentielle sur les cinq derniers jours.
    – L’Espagne a un point bas aujourd’hui. Mais un point anormal ne permet pas de considérer qu’il s’agit d’un changement de tendance.
    – En France, malheureusement, la courbe reste toujours une progression fidèle à l’évolution exponentielle.

    Sur la seconde courbe, j’ai désormais superposé la France, l’Italie (11 jours plus tôt) et l’Espagne (5 jours plus tôt), ce fois en nombre de décès cumulés. L’Espagne progresse certes légèrement plus rapidement que la France, mais la différence n’est pas énorme. Si l’évolution de la France ne s’infléchit pas rapidement, on risque d’atteindre d’ici une semaine à dix jours les chiffres (encore plus catastrophiques) de l’Espagne et l’Italie (si j’ai suivi l’actualité : les deux pays qui ont désormais les plus grands nombres de décès, supérieurs aux chiffres officiels chinois).

    Note : beaucoup de commentaires aujourd’hui sur le fait que la France ne compte pas un certain nombre de morts (ehpad, à domicile), mais on ne précise jamais si l’Italie et l’Espagne les intègrent ou pas.

    Note 2 : rappel de la discussion suite aux courbes d’hier. Je n’utilise pas les courbes des corrélations exponentielles pour essayer de prédire à moyen terme l’évolution des chiffres, mais :
    – pour montrer l’évolution passée, qui a été exponentielle, ou qui l’est toujours selon les pays), et donc éventuellement suggérer que les tout prochains jours devraient rester dans cette tendance (pour la France notamment),
    – surtout essayer de visualiser les infléchissements attendus dans l’évolution d’une épidémie, notamment ceux qui devraient découler des confinements. Essayer de détecter la stabilisation de la progression qui mène au plateau, laquelle devrait précéder une baisse de la mortalité. Pour l’Italie notamment, on a depuis 5 jours une forte anomalie par rapport à l’évolution exponentielle de la période précédente.

  • Antibody responses to #SARS-CoV-2 in patients of novel #coronavirus disease 2019
    https://www.medrxiv.org/content/10.1101/2020.03.02.20030189v1.full.pdf

    Le dosage des anticorps aurait une valeur diagnostique et pronostique

    Leur persistance n’a pas été étudiée

    Our results demonstrated an excellent sensitivity of Ab test in detections of patient’s samples after 1-week since onset. Notably, even in the early stages of the illness within 7-day, some patients with negative nucleic acid findings could be screened out through antibody testing. Combining RNA test and antibody test significantly raised the sensitivity for detecting patients (p < 0.001). Above findings indicate that the antibody detection be an important supplement to RNA detection during the illness course.

    The results suggested that a high titer of total antibodies against the virus may be considered as a risk factor of critical illness, independently from older age, male gender and comorbidities (Table 4).

    It should be noted that there were some limitations of this study. First, for most of RNA tests of the patients were based on upper respiratory tract specimens, the positive rate may be higher in detection using lower respiratory tract specimens, such as bronchoalveolar lavage fluid, deep tracheal aspirates, and induced sputum may yield higher sensitivity for RNA tests. Second, we cannot evaluate the persistence of antibodies because samples were collected during the acute illness course of patients.

  • Après six semaines de #confinement, la #Chine entrevoit le printemps | L’Humanité
    https://www.humanite.fr/apres-six-semaines-de-confinement-la-chine-entrevoit-le-printemps-686139

    Un tournant est engagé dans la lutte contre l’épidémie du #coronavirus. Le 19 mars, et pour la première fois depuis le début de l’épidémie, aucun nouveau cas de contamination « locale » au Covid-19 n’a été enregistré dans le pays. Les autorités redoutent toutefois que l’épidémie ne connaisse une seconde vague avec l’entrée de personnes contaminées sur le territoire. La semaine dernière, les autorités annonçaient également une reprise progressive de l’activité. Mais les inconnues sur le plan international continuent de peser.

    #covid-19 #sars-cov-2