Rapid and accurate identification of SARS-CoV-2 variants containing E484 mutation

The ongoing coronavirus disease 2019(COVID-19)pandemic caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection has led to over 240 million confirmed infections and severe economic burdens worldwide.Multiple emerging SARS-CoV-2 variants of concern(VOCs)and variants of interest(VOIs)have recently beenidentifiedand are nowspreading internationally,including B.1.1.7(Alpha),B.1.351(Beta),P.1(Gamma),B.1.617(Delta and Kappa),C.37(Lambda),and B.1.621(Mu),all of which appear to bemore easily transmitted(WHO,COVID-19Weekly EpidemiologicalUpdate).Beta andGamma VOCs can seriously impair the protective efficacy of existing vaccines,potentially precluding the possibility of attaining"herd immunity."

Factors Associated with SARS-CoV-2 Repeat Positivity—Beijing,China,June–September 2020

Introduction:Repeat positive severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)following COVID-19 initial viral clearance(repositivity)poses a public health management challenge.The objective was to determine factors associated with neutralizing antibody(Nab)level and re-positivity among patients infected with a single strain SARS-CoV-2.Methods:During a single strain SARS-CoV-2 cluster in Beijing,China,longitudinal individual clinical,virological,and immunological data were collected from 368 infections from June 13 to September 22,2020.Factors associated with Nab level and re-positivity were analyzed using generalized estimating equations.Results:A total of 353(96%)SARS-CoV-2 infections had demographic,clinical,and laboratory data available.Among the 353 infections,55(15.5%)were re-positive,and blood draws were taken from 346 individuals(98.0%)during hospitalization and/or during the follow-up period.Symptoms were milder for the second-time admission for the re-positives,although 36.4%of re-positives presented with radiographic appearance of pneumonia manifestation.Compared to non-re-positive patients,NAb titers were lower among re-positives;NAb was positively associated with clinical severity.Samples from the lower respiratory tract manifested higher viral load than that from the upper respiratory tract.Multivariable analysis showed re-positivity was positively associated with being female[odd ratio(OR)=1.7,95%confidence interval(CI)1.1–2.8]and being aged<18 years(OR=5.2,95%CI 1.5–18.1);having initially asymptomatic infection(OR=13.7,95%CI 1.6–116.3);and negatively associated with a higher NAb level(OR=0.9,95%CI 0.5–1.7).Conclusions:NAb may be important for sustained viral clearance.Lower respiratory tract infection was associated with higher viral load among all infections when compared to upper respiratory tract infection.Continuous lower respiratory and intermittent upper respiratory viral shedding among COVID-19 infections may occur.