J. Broach

Bio: J. Broach is an academic researcher. The author has contributed to research in topics: Medicine & Test (biology). The author has an hindex of 1, co-authored 1 publications receiving 1501 citations.

Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness

Abstract: The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimated viral expansion and clearance rates and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to ‘superspreading’. Viral genome loads often peaked days earlier in saliva than in nasal swabs, indicating strong tissue compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of Alpha (B.1.1.7) and previously circulating non-variant-of-concern viruses were mostly indistinguishable, indicating that the enhanced transmissibility of this variant cannot be explained simply by higher viral loads or delayed clearance. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading. A longitudinal analysis of viral expansion and clearance rates in 60 individuals sampled daily during acute infection reveals high inter-individual variation in infectious virus shedding, which may contribute to superspreading.

Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveals Limited Infectious Virus Shedding and Restricted Tissue Distribution

Abstract: Abstract Background The global effort to vaccinate people against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during an ongoing pandemic has raised questions about how vaccine breakthrough infections compare with infections in immunologically naive individuals and the potential for vaccinated individuals to transmit the virus. Methods We examined viral dynamics and infectious virus shedding through daily longitudinal sampling in 23 adults infected with SARS-CoV-2 at varying stages of vaccination, including 6 fully vaccinated individuals. Results The durations of both infectious virus shedding and symptoms were significantly reduced in vaccinated individuals compared with unvaccinated individuals. We also observed that breakthrough infections are associated with strong tissue compartmentalization and are only detectable in saliva in some cases. Conclusions Vaccination shortens the duration of time of high transmission potential, minimizes symptom duration, and may restrict tissue dissemination.

Comparison of Rapid Antigen Tests' Performance between Delta (B.1.61.7; AY.X) and Omicron (B.1.1.529; BA1) Variants of SARS-CoV-2: Secondary Analysis from a Serial Home Self-Testing Study

Abstract: Background: There is a need to understand the performance of rapid antigen tests (Ag-RDT) for detection of the Delta (B.1.61.7; AY.X) and Omicron (B.1.1.529; BA1) SARS-CoV-2 variants. Methods: Participants without any symptoms were enrolled from October 18, 2021 to January 24, 2022 and performed Ag-RDT and RT-PCR tests every 48 hours for 15 days. This study represents a non-pre-specified analysis in which we sought to determine if sensitivity of Ag-RDT differed in participants with Delta compared to Omicron variant. Participants who were positive on RT-PCR on the first day of the testing period were excluded. Delta and Omicron variants were defined based on sequencing and date of first RT-PCR positive result (RT-PCR+). Comparison of Ag-RDT performance between the variants was based on proportion of participants with Ag-RDT+ results in relation to their first RT-PCR+ result. Subsample analysis was performed based on the result of participants' second RT-PCR test within 48 hours of the first RT-PCR+ test. Results: From the 7,349 participants enrolled in the parent study, 5,506 met the eligibility criteria for this study. A total of 153 participants were RT-PCR+ (61 Delta, 92 Omicron); among this group, 36 (23.5%) tested Ag-RDT+ on the same day and 36 (23.5%) tested Ag-RDT+ within 48 hours as first RT-PCR+. The differences between variants were not statistically significant (same-day: Delta 16.4% [95% CI: 8.2-28.1] vs Omicron 28.2% [95% CI: 19.4-38.6; 48-hours: Delta 45.9% [33.1-59.2] vs. Omicron 60.9% [50.1-70.9]). This trend continued among the 86 participants who had consecutive RT-PCR+ result (Delta: 79.3% [60.3-92.1] vs. Omicron: 89.5% [78.5-96.0]). Conversely, the 38 participants who had an isolated positive RT-PCR remained consistently negative on Ag-RDT, regardless of the variant. Conclusions: The performance of Ag-RDT is not inferior among Omicron variant in comparison to the Delta variant. The improvement in sensitivity of Ag-RDT with serial testing is consistent between Delta and Omicron variant. Performance of Ag-RDT varies based on duration of RT-PCR+ results and more studies are needed to understand the clinical and public health significance of individuals who are RT-PCR+ for less than 48 hours.

Comparison of Rapid Antigen Tests' Performance Between Delta and Omicron Variants of SARS-CoV-2

Abstract: Use of rapid tests for diagnosis of COVID-19 is now commonplace, but questions remain regarding their performance characteristics compared with those of polymerase chain reaction testing. The role of sequential rapid testing in improving sensitivity is of great interest.

A performance comparison of multi-hop wireless ad hoc network routing protocols

Abstract: An ad hoc networkis a collwtion of wirelessmobilenodes dynamically forminga temporarynetworkwithouttheuseof anyexistingnetworkirrfrastructureor centralizedadministration.Dueto the limitedtransmissionrange of ~vlrelessnenvorkinterfaces,multiplenetwork“hops”maybe neededfor onenodeto exchangedata ivithanotheracrox thenetwork.Inrecentyears, a ttiery of nelvroutingprotocols~geted specificallyat this environment havebeen developed.but little pcrfomrartwinformationon mch protocol and no ralistic performancecomparisonbehvwrrthem ISavailable. ~Is paper presentsthe results of a derailedpacket-levelsimulationcomparing fourmulti-hopwirelessad hoc networkroutingprotocolsthatcovera range of designchoices: DSDV,TORA, DSR and AODV. \Vehave extended the /~r-2networksimulatorto accuratelymodelthe MACandphysical-layer behaviorof the IEEE 802.1I wirelessLANstandard,includinga realistic wtrelesstransmissionchannelmodel, and present the resultsof simulations of net(vorksof 50 mobilenodes.

A review of current routing protocols for ad hoc mobile wireless networks

Abstract: An ad hoc mobile network is a collection of mobile nodes that are dynamically and arbitrarily located in such a manner that the interconnections between nodes are capable of changing on a continual basis. In order to facilitate communication within the network, a routing protocol is used to discover routes between nodes. The primary goal of such an ad hoc network routing protocol is correct and efficient route establishment between a pair of nodes so that messages may be delivered in a timely manner. Route construction should be done with a minimum of overhead and bandwidth consumption. This article examines routing protocols for ad hoc networks and evaluates these protocols based on a given set of parameters. The article provides an overview of eight different protocols by presenting their characteristics and functionality, and then provides a comparison and discussion of their respective merits and drawbacks.

The broadcast storm problem in a mobile ad hoc network

Abstract: Broadcasting is a common operation in a network to resolve many issues. In a mobile ad hoc network (MANET) in particular, due to host mobility, such operations are expected to be executed more frequently (such as finding a route to a particular host, paging a particular host, and sending an alarm signal). Because radio signals are likely to overlap with others in a geographical area, a straightforward broadcasting by flooding is usually very costly and will result in serious redundancy, contention, and collision, to which we call the broadcast storm problem. In this paper, we identify this problem by showing how serious it is through analyses and simulations. We propose several schemes to reduce redundant rebroadcasts and differentiate timing of rebroadcasts to alleviate this problem. Simulation results are presented, which show different levels of improvement over the basic flooding approach.

Geography-informed Energy Conservation for Ad Hoc Routing

Abstract: We introduce a geographical adaptive fidelity (GAF) algorithm that reduces energy consumption in ad hoc wireless networks. GAF conserves energy by identifying nodes that are equivalent from a routing perspective and turning off unnecessary nodes, keeping a constant level of routing fidelity. GAF moderates this policy using application- and system-level information; nodes that source or sink data remain on and intermediate nodes monitor and balance energy use. GAF is independent of the underlying ad hoc routing protocol; we simulate GAF over unmodified AODV and DSR. Analysis and simulation studies of GAF show that it can consume 40% to 60% less energy than an unmodified ad hoc routing protocol. Moreover, simulations of GAF suggest that network lifetime increases proportionally to node density; in one example, a four-fold increase in node density leads to network lifetime increase for 3 to 6 times (depending on the mobility pattern). More generally, GAF is an example of adaptive fidelity, a technique proposed for extending the lifetime of self-configuring systems by exploiting redundancy to conserve energy while maintaining application fidelity.

SPINS: security protocols for sensor networks

Abstract: As sensor networks edge closer towards wide-spread deployment, security issues become a central concern. So far, much research has focused on making sensor networks feasible and useful, and has not concentrated on security.We present a suite of security building blocks optimized for resource-constrained environments and wireless communication. SPINS has two secure building blocks: SNEP and mTESLA SNEP provides the following important baseline security primitives: Data confidentiality, two-party data authentication, and data freshness. A particularly hard problem is to provide efficient broadcast authentication, which is an important mechanism for sensor networks. mTESLA is a new protocol which provides authenticated broadcast for severely resource-constrained environments. We implemented the above protocols, and show that they are practical even on minimal hardware: the performance of the protocol suite easily matches the data rate of our network. Additionally, we demonstrate that the suite can be used for building higher level protocols.