Understanding the particle size distribution in the air and patterns of environmental contamination of SARS-CoV-2 is essential for infection prevention policies. Here we screen surface and air samples from hospital rooms of COVID-19 patients for SARS-CoV-2 RNA. Environmental sampling is conducted in three airborne infection isolation rooms (AIIRs) in the ICU and 27 AIIRs in the general ward. 245 surface samples are collected. 56.7% of rooms have at least one environmental surface contaminated. High touch surface contamination is shown in ten (66.7%) out of 15 patients in the first week of illness, and three (20%) beyond the first week of illness (p = 0.01, χ2 test). Air sampling is performed in three of the 27 AIIRs in the general ward, and detects SARS-CoV-2 PCR-positive particles of sizes >4 µm and 1–4 µm in two rooms, despite these rooms having 12 air changes per hour. This warrants further study of the airborne transmission potential of SARS-CoV-2.

Background Key knowledge gaps remain in the understanding of viral dynamics and immune response of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. Methods We evaluated these characteristics and established their association with clinical severity in a prospective observational cohort study of 100 patients with PCR-confirmed SARS-CoV-2 infection (mean age, 46 years; 56% male; 38% with comorbidities). Respiratory samples (n = 74) were collected for viral culture, serum samples for measurement of IgM/IgG levels (n = 30), and plasma samples for levels of inflammatory cytokines and chemokines (n = 81). Disease severity was correlated with results from viral culture, serologic testing, and immune markers. Results Fifty-seven (57%) patients developed viral pneumonia, of whom 20 (20%) required supplemental oxygen, including 12 (12%) with invasive mechanical ventilation. Viral culture from respiratory samples was positive for 19 of 74 patients (26%). No virus was isolated when the PCR cycle threshold (Ct) value was >30 or >14 days after symptom onset. Seroconversion occurred at a median (IQR) of 12.5 (9–18) days for IgM and 15.0 (12–20) days for IgG; 54/62 patients (87.1%) sampled at day 14 or later seroconverted. Severe infections were associated with earlier seroconversion and higher peak IgM and IgG levels. Levels of IP-10, HGF, IL-6, MCP-1, MIP-1α, IL-12p70, IL-18, VEGF-A, PDGF-BB, and IL-1RA significantly correlated with disease severity. Conclusions We found virus viability was associated with lower PCR Ct value in early illness. A stronger antibody response was associated with disease severity. The overactive proinflammatory immune signatures offer targets for host-directed immunotherapy, which should be evaluated in randomized controlled trials.

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Background The performance of rRT-PCR for SARS-CoV-2 varies with sampling site(s), illness stage and infection site. Methods Unilateral nasopharyngeal, nasal mid-turbinate, throat swabs, and saliva were simultaneously sampled for SARS-CoV-2 rRT-PCR from suspect or confirmed cases of COVID-19.True positives were defined as patients with at least one SARS-CoV-2 detected by rRT-PCR from any site on the evaluation day or at any time point thereafter, till discharge. Diagnostic performance was assessed and extrapolated for site combinations. Results We evaluated 105 patients; 73 had active SARS-CoV-2 infection. Overall, nasopharyngeal specimens had the highest clinical sensitivity at 85%, followed by throat, 80%, mid-turbinate, 62%, and saliva, 38-52%. Clinical sensitivity for nasopharyngeal, throat, mid-turbinate and saliva was 95%, 88%, 72%, and 44-56% if taken ≤7 days from onset of illness, and 70%, 67%, 47%, 28-44% if >7 days of illness. Comparing patients with URTI vs. pneumonia, clinical sensitivity for nasopharyngeal, throat, mid-turbinate and saliva was 92% vs 70%, 88% vs 61%, 70% vs 44%, 43-54% vs 26-45%. A combination of nasopharyngeal plus throat or mid-turbinate plus throat specimen afforded overall clinical sensitivities of 89-92%, this rose to 96% for persons with URTI and 98% for persons <7 days from illness onset. Conclusion Nasopharyngeal followed by throat specimens offer the highest clinical sensitivity for COVID-19 diagnosis in early illness. Clinical sensitivity improves and is similar when either mid-turbinate or nasopharyngeal specimens are combined with throat specimens. Upper respiratory specimens perform poorly if taken after the first week of illness or if there is pneumonia.

bacteremia is caused mainly by sequence type complex 131 (STc131) and two clades within its fluoroquinolone-resistance-associated 30 subclone,30R1 and 30Rx. We examined clinical and molecular correlates of bacteremia in two geographically distinct centers. We retrospectively studied 251 unique bloodstream isolates from 246 patients (48 from the Mayo Clinic, Rochester, MN [MN], and 198 from Tan Tock Seng Hospital, Singapore [SG]), from October 2013 through March 2014. Isolates underwent PCR for phylogroup, STc, type, and virulence gene profiles, and medical records were reviewed. Although STc131 accounted for 25 to 27% of all bacteremia isolates at each site, its extended-spectrum-β-lactamase (ESBL)-associated30Rx clade was more prominent in SG than in MN (15% versus 4%; = 0.04). In SG only, patients with STc131 (versus other STc isolates) were more likely to receive inactive initial antibiotics (odds ratio, 2.8; = 0.005); this was true specifically for patients with30Rx (odds ratio, 7.0; = 0.005).30Rx comprised 16% of community-onset bacteremia episodes in SG but none in MN. In SG, virulence scores were higher for 30Rx than for30R1, non-30 STc131, and non-STc131 isolates ( < 0.02 for all comparisons). At neither site did mortality differ by clonal status. The ESBL-associated 30Rx clade was more prevalent and more often of community onset in SG, where it predicted inactive empirical treatment. The clonal distribution varies geographically and has potentially important clinical implications. Rapid susceptibility testing and clonal diagnostics for30/30Rx might facilitate earlier prescribing of active therapy.