In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants.

SARS-CoV-2 has undergone repeated and rapid evolution to circumvent host immunity. However, outside of prolonged infections in immunocompromised hosts, within-host positive selection has rarely been detected. The low diversity within-hosts and strong genetic linkage among genomic sites make accurately detecting positive selection difficult.

Asymptomatic and mildly symptomatic influenza virus infections by season --Case-ascertained household transmission studies, United States, 2017-2023.

Asymptomatic influenza virus infection occurs but may vary by factors such as age, vaccination status, or season. We examined the frequency of influenza virus infection and symptoms using data from two case-ascertained household transmission studies (2017-2023) with prospective, systematic collection of respiratory specimens and symptoms. From the 426 influenza virus infected household contacts that met our inclusion criteria, 8% were asymptomatic, 6% had non-respiratory symptoms, 23% had acute respiratory symptoms, and 62% had influenza-like illness symptoms.

Estimated Effectiveness of Influenza Vaccines in Preventing Secondary Infections in Households.

Importance: Influenza vaccine effectiveness (VE) is commonly assessed against prevention of illness that requires medical attention. Few studies have evaluated VE against secondary influenza infections.

Objective: To determine the estimated effectiveness of influenza vaccines in preventing secondary infections after influenza was introduced into households.

Identifying potential introduced and natural sources of pollution in Delaware watersheds.

Managing water quality with microbial impairment caused by poses unique challenges regarding the determination of fecal host origin. Most water monitoring is performed based on counts that neither detect the location of the introduction of pollution nor identify the type of contaminating . The use of sequenced-based microbial source tracking could allow for identification of fecal origin and potential remediation of pollution.

Influenza virus shedding and symptoms: Dynamics and implications from a multiseason household transmission study.

Isolation of symptomatic infectious persons can reduce influenza transmission. However, virus shedding that occurs without symptoms will be unaffected by such measures. Identifying effective isolation strategies for influenza requires understanding the interplay between individual virus shedding and symptom presentation.