Multiple Transmission Networks Research Articles

Maximizing the impact of limited vaccine supply under different early epidemic conditions: a 2-city modelling analysis of monkeypox virus transmission among men who have sex with men.

The current global monkeypox virus (MPXV) outbreak has disproportionately affected gay, bisexual and other men who have sex with men (GBMSM). Given that many jurisdictions have been faced with limited supplies of MPXV vaccine, we aimed to explore optimal vaccine allocation between 2 linked GBMSM transmission networks over a short-term time horizon, across several epidemic conditions. We constructed a deterministic compartmental MPXV transmission model. We parameterized the model to reflect 2 representative, partially connected GBMSM sexual networks ( cities), using 2022 data from Ontario. We simulated a roll-out of 5000 vaccine doses over 30 days that started 45 days after epidemic seeding with 10 imported cases. Within this model, we varied the relative city (network) sizes, epidemic potentials (R 0), between-city mixing and distribution of seed cases between cities. For each combination of varied factors, we identified the allocation of doses between cities that maximized infections averted by day 90. Under our modelling assumptions, we found that a limited MPXV vaccine supply could generally avert more early infections when prioritized to networks that were larger, had more initial infections or had greater R 0. Greater between-city mixing decreased the influence of initial seed cases and increased the influence of city R 0 on optimal allocation. Under mixed conditions (e.g., fewer seed cases but greater R 0), optimal allocation required doses shared between cities. In the context of the current global MPXV outbreak, we showed that prioritization of a limited supply of vaccines based on network-level factors can help maximize infections averted during an emerging epidemic. Such prioritization should be grounded in an understanding of context-specific risk drivers and should acknowledge potential connectedness of multiple transmission networks.

Solving Bilevel AC OPF Problems by Smoothing the Complementary Conditions – Part II: Solution Techniques and Case Study

This is a second part of the research on AC optimal power flow being used in the lower level of the bilevel strategic bidding or investment models. As an example of a suitable upper-level problem, we observe a strategic bidding of energy storage and propose a novel formulation based on the smoothing technique. After presenting the idea and scope of our work, as well as the model itself and the solution algorithm in the companion paper (Part I), this paper presents a number of existing solution techniques and the proposed one based on smoothing the complementary conditions. The superiority of the proposed algorithm and smoothing techniques is demonstrated in terms of accuracy and computational tractability over multiple transmission networks of different sizes and different OPF models. The results indicate that the proposed approach outperforms all other options in both metrics by a significant margin. This is especially noticeable in the metric of accuracy where out of total 422 optimizations over 9 meshed networks the greatest AC OPF error is 0.023% that is further reduced to 3.3e-4% in the second iteration of our algorithm.

New Subtype B Containing HIV-1 Circulating Recombinant of sub-Saharan Africa Origin in Nigerian Men Who Have Sex With Men.

HIV-1 circulating recombinant forms (CRF) containing subtype B are uncommon in sub-Saharan Africa. Prevalent infections observed during enrollment of a prospective study of men who have sex with men (MSM) from Lagos, Nigeria, revealed the presence of a family of subtype B and CRF02_AG recombinants. This report describes the HIV-1 genetic diversity within a high-risk, high-prevalence, and previously undersampled cohort of Nigerian MSM. Between 2013 and 2016, 672 MSM were enrolled at the Lagos site of the TRUST/RV368 study. Prevalent HIV-1 infections were initially characterized by pol sequencing and phylogenetic subtyping analysis. Samples demonstrating the presence of subtype B were further characterized by near full-length sequencing, phylogenetic, and Bayesian analyses. Within this cohort, HIV-1 prevalence was 59%. The major subtype was CRF02_AG (57%), followed by CRF02/B recombinants (15%), subtype G (13%), and smaller amounts of A1, B, and other recombinants. Nine clusters of closely related pol sequences indicate ongoing transmission events within this cohort. Among the CRF02_AG/B, a new CRF was identified and termed CRF95_02B. Shared risk factors and Bayesian phylogenetic inference of the new CRF95_02B and the similarly structured CRF56_cpx indicate a Nigerian or West African origin of CRF56_cpx before its observation in France. With high HIV-1 prevalence, new strains, and multiple transmission networks, this cohort of Nigerian MSM represents a previously hidden reservoir of HIV-1 strains, including the newly identified CRF95_02B and closely related CRF56_cpx. These strains will need to be considered during vaccine selection and development to optimize the design of a globally effective HIV-1 vaccine.

Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak.

BackgroundUntil recently, Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks.MethodsAll KPC-producing Enterobacteriaceae isolates referred to the state reference laboratory from 2012 onwards were included. Whole-genome sequencing was performed in parallel with a detailed descriptive epidemiological investigation of each case, using Illumina sequencing on each isolate. This was complemented with PacBio long-read sequencing on selected isolates to establish high-quality reference sequences and interrogate characteristics of KPC-encoding plasmids.ResultsInitial investigations indicated that the outbreak was widespread, with 86 KPC-producing Enterobacteriaceae isolates (K. pneumoniae 92%) identified from 35 different locations across metropolitan and rural Victoria between 2012 and 2015. Initial combined analyses of the epidemiological and genomic data resolved the outbreak into distinct nosocomial transmission networks, and identified healthcare facilities at the epicentre of KPC transmission. New cases were assigned to transmission networks in real-time, allowing focussed infection control efforts. PacBio sequencing confirmed a secondary transmission network arising from inter-species plasmid transmission. Insights from Bayesian transmission inference and analyses of within-host diversity informed the development of state-wide public health and infection control guidelines, including interventions such as an intensive approach to screening contacts following new case detection to minimise unrecognised colonisation.ConclusionA real-time combined epidemiological and genomic investigation proved critical to identifying and defining multiple transmission networks of KPC Enterobacteriaceae, while data from either investigation alone were inconclusive. The investigation was fundamental to informing infection control measures in real-time and the development of state-wide public health guidelines on carbapenemase-producing Enterobacteriaceae surveillance and management.

Neisseria gonorrhoeae population in Arkhangelsk, Russia: phenotypic and genotypic heterogeneity

Reliable data concerning the incidence and phenotypic and genotypic characteristics of the Neisseria gonorrhoeae population in many eastern European countries are lacking. Clinically significant N. gonorrhoeae isolates (n = 76) from 76 consecutive patients in Arkhangelsk, Russia were characterised by antimicrobial susceptibility testing, serovar determination, porB gene sequencing and N. gonorrhoeae multi-antigen sequence typing (NG-MAST). The isolates were assigned to 12 different serovars, displayed 35 divergent porB sequences, and belonged to 40 different sequence types (STs). All the serovars, but only seven of the STs, had been identified previously in other countries. Twelve ST clusters of between two and 14 isolates were identified, which indicated that many multiple transmission networks exist in Arkhangelsk. The high number of unique STs (n = 28) may be a consequence of sub-optimal diagnostic procedures, ineffective partner tracing, local emergence of new STs, import of strains via sexual tourists, or foreign travel. The N. gonorrhoeae population circulating in Arkhangelsk was highly diverse and differed from the N. gonorrhoeae populations disseminated in some western European countries. Thorough knowledge concerning the incidence of gonorrhoea, antibiotic susceptibility and other phenotypic and genotypic characteristics of the N. gonorrhoeae strains circulating in eastern Europe is crucial.