A long-standing question in infectious disease dynamics concerns the role of transmission heterogeneities, driven by demography, behavior and interventions. Based on detailed patient and contact tracing data in Hunan, China we find 80% of secondary infections traced back to 15% of SARS-CoV-2 primary infections, indicating substantial transmission heterogeneities. Transmission risk scales positively with the duration of exposure and the closeness of social interactions and is modulated by demographic and clinical factors. The lockdown period increases transmission risk in the family and households, while isolation and quarantine reduce risks across all types of contacts. The reconstructed infectiousness profile of a typical SARS-CoV-2 patient peaks just before symptom presentation. Modeling indicates SARS-CoV-2 control requires the synergistic efforts of case isolation, contact quarantine, and population-level interventions, owing to the specific transmission kinetics of this virus.

Several mechanisms driving SARS-CoV-2 transmission remain unclear. Based on individual records of 1178 potential SARS-CoV-2 infectors and their 15,648 contacts in Hunan, China, we estimated key transmission parameters. The mean generation time was estimated to be 5.7 (median: 5.5, IQR: 4.5, 6.8) days, with infectiousness peaking 1.8 days before symptom onset, with 95% of transmission events occurring between 8.8 days before and 9.5 days after symptom onset. Most transmission events occurred during the pre-symptomatic phase (59.2%). SARS-CoV-2 susceptibility to infection increases with age, while transmissibility is not significantly different between age groups and between symptomatic and asymptomatic individuals. Contacts in households and exposure to first-generation cases are associated with higher odds of transmission. Our findings support the hypothesis that children can effectively transmit SARS-CoV-2 and highlight how pre-symptomatic and asymptomatic transmission can hinder control efforts.

A long-standing question in infectious disease dynamics is the role of transmission heterogeneities, particularly those driven by demography, behavior and interventions. Here we characterize transmission risk between 1,178 SARS-CoV-2 infected individuals and their 15,648 close contacts based on detailed contact tracing data from Hunan, China. We find that 80% of secondary transmissions can be traced back to 14% of SARS-CoV-2 infections, indicating substantial transmission heterogeneities. Regression analysis suggests a marked gradient of transmission risk scales positively with the duration of exposure and the closeness of social interactions, after adjusted for demographic and clinical factors. Population-level physical distancing measures confine transmission to families and households; while case isolation and contact quarantine reduce transmission in all settings. Adjusted for interventions, the reconstructed infectiousness profile of a typical SARS-CoV-2 infection peaks just before symptom presentation, with ~50% of transmission occurring in the pre-symptomatic phase. Modelling results indicate that achieving SARS-CoV-2 control would require the synergistic efforts of case isolation, contact quarantine, and population-level physical distancing measures, owing to the particular transmission kinetics of this virus.

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Importance Several parameters driving the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain unclear, including age-specific differences in infectivity and susceptibility, and the contribution of inapparent infections to transmission. Robust estimates of key time-to-event distributions remain scarce as well. Objective Illustrate SARS-CoV-2 transmission patterns and risk factors, and estimate key time-to-event distributions. Design, Setting, and Participants Individual-based data on 1,178 SARS-CoV-2 infected individuals and their 15,648 contacts identified by contact tracing monitoring over the period from January 13-April 02, 2020 were extracted from the notifiable infectious diseases reporting system in Hunan Province, China. Demographic characteristics, severity classification, exposure and travel history, and key clinical timelines were retrieved. Exposures Confirmed SARS-CoV-2 infection by positive polymerase chain reaction test result of respiratory samples, and exposure to SARS-CoV-2 infected individuals via household, relative, social, and other types of contacts. Main Outcomes and Measures The relative contribution of pre-symptomatic and asymptomatic transmission, key time-to-event parameters, and the effect of biological, demographic, and behavioral factors on SARS-CoV-2 infectivity and susceptibility were quantified. Results Among SARS-CoV-2 infected individuals, the estimated mean serial interval was 5.5 days (95%CI -5.0, 19.9) and the mean generation time was 5.5 days (95%CI 1.7, 11.6). Infectiousness was estimated to peak 1.8 days before symptom onset, with 95% of transmission events occurring between -7.6 days and 7.3 days from the date of symptom onset. The proportion of pre-symptomatic transmission was estimated at 62.5%, while a lower bound for the proportion of asymptomatic transmission was 3.5%. Infectiousness of SARS-CoV-2 was not significantly different between working-age adults (15-59 years old) and other age groups (0-14 years old: p-value=0.16; 60 years and over: p-value=0.33), whilst susceptibility to SARS-CoV-2 infection was estimated to increase with age (p-value=0.03). In addition, transmission risk was higher for household contacts (p-value<0.001), but decreased in later generations of a cluster (second generation: OR=0.13, p-value<0.001; generations 3-4: OR=0.05, p-value<0.001, relative to generation 1) and for those exposed to infectors with a larger number of contacts (p-value=0.04). Conclusions and Relevance These findings support the contribution of children to transmission and the importance of pre-symptomatic transmission, in turn highlighting the importance of large-scale testing, contact tracing activities, and the use of personnel protective equipment during the COVID-19 pandemic.

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Background Globally, the epidemiology of non‐SARS‐CoV‐2 respiratory viruses like respiratory syncytial virus (RSV) and influenza virus was remarkably influenced by the implementation of non‐pharmacological interventions (NPIs) during the COVID‐19 pandemic. Our study explored the epidemiological and clinical characteristics of pediatric patients hospitalized with RSV or influenza infection before and during the pandemic after relaxation of NPIs in central China. Methods This hospital‐based prospective case‐series study screened pediatric inpatients (age ≤ 14 years) enrolled with acute respiratory infections (ARI) for RSV or influenza infection from 2018 to 2021. The changes in positivity rates of viral detection, epidemiological, and clinical characteristics were analyzed and compared. Results Median ages of all eligible ARI patients from 2018–2019 were younger than those from 2020–2021, so were ages of cases infected with RSV or influenza (RSV: 4.2 months vs. 7.2 months; influenza: 27.3 months vs. 37.0 months). Where the positivity rate for influenza was considerably decreased in 2020–2021 (1.4%, 27/1964) as compared with 2018–2019 (2.9%, 94/3275, P < 0.05), it was increased for RSV (11.4% [372/3275] vs. 13.3% [262/1964], P < 0.05) in the same period. The number of severe cases for both RSV and influenza infection were also decreased in 2020–2021 compared with 2018–2019. Conclusions The implemented NPIs have had varied impacts on common respiratory viruses. A more effective prevention strategy for RSV infections in childhood is needed.

Background: Mainland China has experienced five epidemics of human cases of avian influenza A(H7N9) virus infection since 2013. We conducted a prospective study to assess long-term clinical, pulmonary function testing, and chest computed tomography (CT) imaging findings after patients were discharged from hospital. Methods: A(H7N9) survivors in five provinces and one municipality underwent follow-up visits from August 2013 to September 2018, at three, six, and 12 months after illness onset, and a subset was also assessed at 18 and 64 months after onset. Thirteen patients were enrolled from the first A(H7N9) epidemic in 2013, 36 from the 2013-2014 second epidemic, and 12 from the 2016-2017 fifth epidemic. At each visit, A(H7N9) survivors received a medical examination, including the mMRC (modified Medical Research Council) dyspnea scale assessment, chest auscultation, pulmonary function testing and chest CT scans. Findings: The median age of 61 A(H7N9) survivors was 50 years. The cumulative rate of pulmonary dysfunction was 38¢5% and 78¢2% for chest CT scan abnormalities at the end of follow-up. Restrictive ventilation dysfunction was common during follow-up. Mild dyspnea was documented at three to 12-month follow-up visits. Interpretation: Patients who survived severe illness from A(H7N9) virus infection had evidence of persistent lung damage and long-term pulmonary dysfunction.