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The circulation of P.1 SARS-CoV-2 lineage becomes a challenge of pandemic control. Among the COVID-19 cases reported in Brazil, P.1 is estimated 54% more fatal than non-P.1 significantly. Considering the transmission advantage of P.1, we raise concerns regarding the rapid growth in critical patients.

The emerging N501Y mutation in severe acute respiratory syndrome coronavirus 2, which becomes prevalent in the UK rapidly, is one of the major challenges of COVID-19 control. To explore the transmission advantage, we estimate that the N501Y substitution increases the infectivity by 52% (95% confidence interval: 46, 58) in terms of the reproduction number.

Background Understanding local epidemiology and etiologies of community-acquired pneumonia in hospitalized patients is crucial for determining the appropriateness of treatment guidelines. We aim to determine the etiologies, severity, and outcomes in adults hospitalized for community-acquired pneumonia and to study the impact of empirical antibiotic therapy on patient outcomes. Methods We performed a prospective observational cohort study involving adults hospitalized for community-acquired pneumonia in Hong Kong. Sputum, nasopharyngeal aspirate, blood, and urine were collected for bacterial culture, molecular tests for detection of viruses and atypical pathogens, and antigen tests. Multivariable logistic regression model and Cox proportional hazard models were performed to determine independent factors associated with prolonged hospitalization and mortality. Results From February 2017 to July 2018, 258 patients were enrolled. The median age was 73 (interquartile range, 61–80) years, 66% were male, 57% had underlying chronic illnesses, 13% had CURB-65 score ≥3, and 10% had higher 1-year mortality. Pathogens were identified in 45% of patients; 20% had viral, 15% had bacterial, and 9% had polymicrobial pneumonia. Streptococcus pneumoniae (12%), influenza virus (12%), and Mycoplasma pneumoniae (1.2%) were the most common bacterial, viral, and atypical pathogens, respectively. Nonadherence to local empirical antibiotic treatment guidelines (primarily recommending beta-lactam and doxycycline) was observed in 25% and was independently associated with prolonged hospitalization (≥7 days) and higher mortality, after adjustment for age, underlying chronic illness, and disease severity. Conclusions Adherence to treatment guidelines was associated with shorter hospitalization and improved survival. We provided evidence for the use of doxycycline for coverage of atypical pathogens in nonsevere pneumonia., In this prospective study involving adults hospitalized with community-acquired pneumonia, adherence to treatment guidelines was independently associated with shorter hospitalization and improved survival. Our findings provided evidence for atypical pathogen coverage with doxycycline, which was less evaluated in other cohorts.