[Aspects virologiques, diagnostic et variants du SARS-CoV-2]

VIROLOGICAL ASPECTS, DIAGNOSTIC TOOLS AND VARIANTS OF SARS-COV-2 SARS-CoV-2 is an enveloped non-segmented linear single-stranded positive RNA virus. The envelope carries the protein spike (S) which recognizes the ACE2 receptor on the target cell and allows entry of the virus. The numerous mutations on the S protein are at the origin of a great genetic diversity, involved in the species barrier and the escape from neutralizing antibodies. The main mode of transmission is respiratory. The virus replicates 24 hours after infection and the viral RNA is detected by direct diagnostic techniques as the reference technique is RT-PCR on a nasopharyngeal sample. To expand screening, RT-PCR on saliva samples and antigenic tests have been developed. The majority of patients develop specific antibodies within 10-15 days which are detectable by serological methods. It is recommended to combine the search for anti-N and anti-S antibodies. The viral genome has great plasticity and variants emerged from the summer of 2020. There are several classifications, including that of the WHO, which assigns each variant a Greek letter. Finally, Sante publique France has deployed an epidemiological surveillance system of variants using PCR screening and sequencing.

Risk factors associated with COVID-19-associated pulmonary aspergillosis in ICU patients: a French multicentric retrospective cohort

OBJECTIVES: The main objective of this study was to determine the incidence of invasive pulmonary aspergillosis (IPA) in patients with coronavirus disease 2019 (COVID-19) admitted to the intensive care unit (ICU), and to describe the patient characteristics associated with IPA occurrence and to evaluate its impact on prognosis. METHODS: We conducted a retrospective cohort study including all successive COVID-19 patients, hospitalized in four ICUs, with secondary deterioration and one or more respiratory samples sent to the mycology department. We used a strengthened IPA testing strategy including seven mycological criteria. Patients were classified as probable IPA according to the European Organization for Research and Treatment of Cancer (EORTC)/Mycoses Study Group Education and Research Consortium (MSGERC) classification if immunocompromised, and according to the recent COVID-19-associated IPA classification otherwise. RESULTS: Probable IPA was diagnosed in 21 out of the 366 COVID-19 patients (5.7%) admitted to the ICU and in the 108 patients (19.4%) who underwent respiratory sampling for deterioration. No significant differences were observed between patients with and without IPA regarding age, gender, medical history and severity on admission and during hospitalization. Treatment with azithromycin for >=3 days was associated with the diagnosis of probable IPA (odds ratio 3.1, 95% confidence interval 1.1-8.5, p = 0.02). A trend was observed with high-dose dexamethasone and the occurrence of IPA. Overall mortality was higher in the IPA patients (15/21, 71.4% versus 32/87, 36.8%, p < 0.01). CONCLUSION: IPA is a relatively frequent complication in severe COVID-19 patients and is responsible for increased mortality. Azithromycin, known to have immunomodulatory properties, may contribute to increase COVID-19 patient's susceptibility to IPA.

Evaluation of the COVID-19 IgG/IgM rapid test from Orient Gene Biotech. (Special Issue: Diagnostic testing for severe acute respiratory syndrome coronavirus 2 and lessons from this pandemic.)

While the coronavirus disease 2019 (COVID-19) pandemic has peaked in many countries already, the current challenge is to assess population immunity on a large scale. Many serological tests are available and require urgent independent validation. Here, we report performance characteristics of Orient Gene Biotech COVID-19 IgG/IgM Rapid Test Cassette (OG) and compare it to Abbott SARS-CoV-2 IgG immunoassay (ASIA). Patients (n = 102) with a positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcriptase PCR (RT-PCR) were tested. The patients were asymptomatic (n = 2) or had mild (n = 37) or severe symptoms requiring hospitalization in a medical unit (n = 35) or intensive care unit (n = 28). Specificity was evaluated for 42 patients with previous viral and parasitic diseases as well as a high level of rheumatic factor. The sensitivity of OG was 95.8% (95% confidence interval [CI95%], 89.6 to 98.8) for samples collected >=10 days after the onset of symptoms, which was equivalent to the sensitivity of ASIA of 90.5% (CI95%, 82.8 to 95.6). OG uncovered six false-negative results of ASIA, of which two had only IgM with OG. Specificity was 100% (CI95%, 93.4 to 100) with both tests on samples, including patients infected with endemic coronavirus. Overall, OG performance characteristics indicate that the test is suitable for routine use in clinical laboratories, and its performance is equivalent to that of immunoassay. Testing OG on a larger asymptomatic population may be needed to confirm these results.

Évaluation du test de diagnostic rapide COVID-19 IgG/IgM (Orient Gene Biotech)

Introduction Tandis que le pic épidémique du COVID-19 semble passé dans la majorité des pays européens, le nouveau challenge est d’évaluer l’immunité de la population à grande échelle. De nombreux tests sérologiques aux performances très variables sont proposés. Il est nécessaire et urgent d’en réaliser la validation qualitative afin de ne pas mésestimer la séroprévalence COVID-19. Nous proposons l’évaluation des performances du test de diagnostic rapide (TDR) Orient Gene (OG) COVID-19 IgG/IgM en comparaison au test ELISA-Abbott SARS-CoV-2 IgG immunoassay (ASIA). Matériels et méthodes Il s’agit d’un test immuno-chromatographique à flux latéral permettant l’obtention d’un résultat en 10minutes. Un total de 102 sérums provenant de patients ayant eu une RT-PCR SARS-CoV-2 positive ont été testé. Ces patients étaient asymptomatiques (n=2), présentaient des symptômes légers (n=37), des symptômes sévères nécessitant l’hospitalisation (n=35) ou ont dû être admis en réanimation (n=28). La spécificité a été évaluée à partir de 42 sérums provenant de patients présentant diverses pathologies virales (dont des coronavirus endémique), parasitaires ou avec un taux de facteur rhumatoïde élevé et prélevé en période pré-pandémique. Résultats La sensibilité de l’OG était de 95,8 % (IC95 %: 89,6–98,8) pour les échantillons collectés ≥10jours après le début des symptômes ce qui était équivalent à la sensibilité 90,5 % (IC95 %: 82,8–95,6) de l’ASIA. L’OG a permis de détecter 6 sérums négatifs en ASIA parmi lesquels 2 présentaient uniquement des IgM sur l’OG. Parmi les 7 sérums négatifs en l’OG, 3 avaient été prélevés moins de 10jours avant le début des symptômes et les 4 autres sérums provenaient de patients présentant des déficits immunitaires acquis pouvant expliquer la négativité du test malgré une PCR positive antérieure. La spécificité était de 100 % (IC95 %: 93,4–100) avec les deux tests. Conclusion Les caractéristiques de l’OG indique que ce TDR est approprié à une utilisation en routine au laboratoire avec une sensibilité équivalente à un test ELISA classique. Ce test s’adapte également à une utilisation ambulatoire en raison de sa facilité d’utilisation. L’évaluation de ce test sur un plus grand nombre de personnes asymptomatiques peut être nécessaire afin de confirmer nos résultats dans cette population.