Last data update: Apr 29, 2024. (Total: 46658 publications since 2009)
Records 1-10 (of 10 Records) |
Query Trace: Charniga K[original query] |
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Nowcasting and forecasting the 2022 U.S. Mpox outbreak: Support for public health decision making and lessons learned
Charniga K , Madewell ZJ , Masters NB , Asher J , Nakazawa Y , Spicknall IH . Epidemics 2024 47 100755 In June of 2022, the U.S. Centers for Disease Control and Prevention (CDC) Mpox Response wanted timely answers to important epidemiological questions which can now be answered more effectively through infectious disease modeling. Infectious disease models have shown to be valuable tools for decision making during outbreaks; however, model complexity often makes communicating the results and limitations of models to decision makers difficult. We performed nowcasting and forecasting for the 2022 mpox outbreak in the United States using the R package EpiNow2. We generated nowcasts/forecasts at the national level, by Census region, and for jurisdictions reporting the greatest number of mpox cases. Modeling results were shared for situational awareness within the CDC Mpox Response and publicly on the CDC website. We retrospectively evaluated forecast predictions at four key phases (early, exponential growth, peak, and decline) during the outbreak using three metrics, the weighted interval score, mean absolute error, and prediction interval coverage. We compared the performance of EpiNow2 with a naïve Bayesian generalized linear model (GLM). The EpiNow2 model had less probabilistic error than the GLM during every outbreak phase except for the early phase. We share our experiences with an existing tool for nowcasting/forecasting and highlight areas of improvement for the development of future tools. We also reflect on lessons learned regarding data quality issues and adapting modeling results for different audiences. |
Updating reproduction number estimates for Mpox in the Democratic Republic of Congo using surveillance data
Charniga K , McCollum AM , Hughes CM , Monroe B , Kabamba J , Lushima RS , Likafi T , Nguete B , Pukuta E , Muyamuna E , Tamfum JM , Karhemere S , Kaba D , Nakazawa Y . Am J Trop Med Hyg 2024 Incidence of human monkeypox (mpox) has been increasing in West and Central Africa, including in the Democratic Republic of Congo (DRC), where monkeypox virus (MPXV) is endemic. Most estimates of the pathogen's transmissibility in the DRC are based on data from the 1980s. Amid the global 2022 mpox outbreak, new estimates are needed to characterize the virus' epidemic potential and inform outbreak control strategies. We used the R package vimes to identify clusters of laboratory-confirmed mpox cases in Tshuapa Province, DRC. Cases with both temporal and spatial data were assigned to clusters based on the disease's serial interval and spatial kernel. We used the size of the clusters to infer the effective reproduction number, Rt, and the rate of zoonotic spillover of MPXV into the human population. Out of 1,463 confirmed mpox cases reported in Tshuapa Province between 2013 and 2017, 878 had both date of symptom onset and a location with geographic coordinates. Results include an estimated Rt of 0.82 (95% CI: 0.79-0.85) and a rate of 132 (95% CI: 122-143) spillovers per year assuming a reporting rate of 25%. This estimate of Rt is larger than most previous estimates. One potential explanation for this result is that Rt could have increased in the DRC over time owing to declining population-level immunity conferred by smallpox vaccination, which was discontinued around 1982. Rt could be overestimated if our assumption of one spillover event per cluster does not hold. Our results are consistent with increased transmissibility of MPXV in Tshuapa Province. |
Possible exposures among mpox patients without reported male-to-male sexual contact - six U.S. Jurisdictions, November 1-December 14, 2022
Sharpe JD , Charniga K , Byrd KM , Stefanos R , Lewis L , Watson J , Feldpausch A , Pavlick J , Hand J , Sokol T , Ortega E , Pathela P , Hennessy RR , Dulcey M , McHugh L , Pietrowski M , Perella D , Shah S , Maroufi A , Taylor M , Cope A , Belay ED , Ellington S , McCollum AM , Zilversmit Pao L , Guagliardo SAJ , Dawson P . MMWR Morb Mortal Wkly Rep 2023 72 (35) 944-948 The extent to which the 2022 mpox outbreak has affected persons without a recent history of male-to-male sexual contact (MMSC) is not well understood. During November 1-December 14, 2022, CDC partnered with six jurisdictional health departments to characterize possible exposures among mpox patients aged ≥18 years who did not report MMSC during the 3 weeks preceding symptom onset. Among 52 patients included in the analysis, 14 (27%) had a known exposure to a person with mpox, including sexual activity and other close intimate contact (eight) and household contact (six). Among 38 (73%) patients with no known exposure to a person with mpox, self-reported activities before illness onset included sexual activity and other close intimate contact (17; 45%), close face-to-face contact (14; 37%), attending large social gatherings (11; 29%), and being in occupational settings involving close skin-to-skin contact (10; 26%). These findings suggest that sexual activity remains an important route of mpox exposure among patients who do not report MMSC. |
Updating reproduction number estimates for mpox in the Democratic Republic of Congo using surveillance data (preprint)
Charniga K , McCollum AM , Hughes CM , Monroe B , Kabamba J , Lushima RS , Likafi T , Nguete B , Pukuta E , Muyamuna E , Tamfum JJM , Karhemere S , Kaba D , Nakazawa Y . medRxiv 2023 17 Incidence of human mpox has been increasing in West and Central Africa, including in the Democratic Republic of Congo (DRC), where monkeypox virus (MPXV) is endemic. Most estimates of the pathogen's transmissibility in DRC are based on data from the 1980s. Amid the global 2022 mpox outbreak, new estimates are needed to characterize the virus' epidemic potential and inform outbreak control strategies. We used the R package vimes to identify clusters of laboratory-confirmed mpox cases in Tshuapa Province, DRC. Cases with both temporal and spatial data were assigned to clusters based on the disease's serial interval and spatial kernel. We used the size of the clusters to infer the effective reproduction number, R<inf>t</inf>, and the rate of zoonotic spillover of MPXV into the human population. Out of 1,463 confirmed mpox cases reported in Tshuapa Province between 2013 and 2017, 878 had both date of symptom onset and a location with geographic coordinates. Results include an estimated R<inf>t</inf> of 0.82 (95% CI: 0.79 - 0.85) and a rate of 132 (95% CI: 122 - 143) spillovers per year assuming a reporting rate of 0.25. This estimate of R<inf>t</inf> is larger compared to most previous estimates. One potential explanation for this result is that R<inf>t</inf> could have increased in DRC over time due to declining population-level immunity conferred by smallpox vaccination, which was discontinued around 1982. R<inf>t</inf> could be overestimated if our assumption of one spillover event per cluster does not hold. Our results are consistent with increased transmissibility of MPXV in Tshuapa Province. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Nowcasting and Forecasting the 2022 U.S. Mpox Outbreak: Support for Public Health Decision Making and Lessons Learned (preprint)
Charniga K , Madewell ZJ , Masters NB , Asher J , Nakazawa Y , Spicknall IH . medRxiv 2023 17 Mpox is a zoonotic disease endemic in Central and West Africa. In May 2022, an outbreak of mpox characterized by human-to-human transmission was detected in multiple non-endemic countries. We performed nowcasting and forecasting for the 2022 mpox outbreak in the United States using the R package EpiNow2. We generated nowcasts/forecasts at the national level, by Census region, and for jurisdictions reporting the greatest number of mpox cases. Modeling results were shared for situational awareness within the Centers for Disease Control and Prevention (CDC) Mpox Response and publicly on the CDC website. We retrospectively evaluated forecast predictions at four key phases during the outbreak using three metrics, the weighted interval score, mean absolute error, and prediction interval coverage. We compared the performance of EpiNow2 with a naive Bayesian generalized linear model (GLM). The EpiNow2 model had less probabilistic error than the GLM during every outbreak phase except for the early phase. We share our experiences with an existing tool for nowcasting/forecasting and highlight areas of improvement for the development of future tools. We also reflect on lessons learned regarding data quality issues and adapting modeling results for different audiences. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Serial interval and incubation period estimates of monkeypox virus infection in 12 U.S. jurisdictions, May - August 2022 (preprint)
Madewell ZJ , Charniga K , Masters NB , Asher J , Fahrenwald L , Still W , Chen J , Kipperman N , Bui D , Shea M , Saathoff-Huber L , Johnson S , Harbi K , Berns AL , Perez T , Gateley E , Spicknall IH , Nakazawa Y , Gift TL . medRxiv 2022 30 Using data collected by 12 U.S. health departments, we report mean estimated serial interval for monkeypox virus infection of 8.5 (95% CrI: 7.3 - 9.9) days for symptom onset from 57 case pairs and mean estimated incubation period of 5.6 (4.3 - 7.8) days from 35 case pairs for symptom onset. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Estimating the incubation period of monkeypox virus during the 2022 multi-national outbreak (preprint)
Charniga K , Masters NB , Slayton RB , Gosdin L , Minhaj FS , Philpott D , Smith D , Gearhart S , Alvarado-Ramy F , Brown C , Waltenburg MA , Hughes CM , Nakazawa Y . medRxiv 2022 23 Monkeypox is a zoonotic disease endemic in Central and West Africa. In May 2022, an outbreak of monkeypox characterized by human-to-human transmission was detected in multiple non-endemic countries. We estimated the incubation period for monkeypox using information from 22 probable (N = 1) and confirmed (N = 21) monkeypox cases in patients reported in the United States through June 6, 2022. We pooled U.S. patient data with the data from 18 confirmed cases in patients reported from the Netherlands through May 31, 2022. The mean incubation period from exposure to first symptom onset was 7.6 days (95% credible interval: 6.2 - 9.7), and the 95th percentile was 17.1 days (95% CrI: 12.7-24.3). These findings align with current CDC recommendations for monitoring close contacts of people with monkeypox for 21 days after their last exposure. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Risk of rabies and implications for postexposure prophylaxis administration in the US
Charniga K , Nakazawa Y , Brown J , Jeon S , Wallace RM . JAMA Netw Open 2023 6 (6) e2317121 IMPORTANCE: In the US, rabies postexposure prophylaxis (PEP) is often administered without a comprehensive and regionally appropriate rabies risk assessment. For low-risk exposures, this can result in patients incurring out-of-pocket expenses or experiencing adverse effects of PEP unnecessarily. OBJECTIVE: To use a model to estimate (1) the probability that an animal would test positive for rabies virus (RABV) given that a person was exposed, and (2) the probability that a person would die from rabies given that they were exposed to a suspect rabid animal and did not receive PEP, and to propose a risk threshold for recommending PEP according to model estimates and a survey. DESIGN, SETTING, AND PARTICIPANTS: In this decision analytical modeling study, positivity rates were calculated using more than 900 000 animal samples tested for RABV between 2011 and 2020. Other parameters were estimated from a subset of the surveillance data and the literature. Probabilities were estimated using Bayes' rule. A survey was administered among a convenience sample of state public health officials in all US states (excluding Hawaii) plus Washington, DC and Puerto Rico to determine a risk threshold for PEP recommendation. Respondents were asked whether they would recommend PEP given 24 standardized exposure scenarios while accounting for local rabies epidemiology. MAIN OUTCOMES AND MEASURES: A quantitative and regionally appropriate approach for helping health care practitioners and public health professionals determine whether to recommend and/or administer rabies PEP. RESULTS: A total of 1728 unique observations were obtained from the model for the probability that an animal would test positive for RABV given that a person was exposed, and 41 472 for ) the probability that a person would die from rabies given that they were exposed to a suspect rabid animal and did not receive PEP. The median probability that an animal would test positive for RABV given that a person was exposed ranged from 3 × 10-7 to 0.97, while the probability that a person would die from rabies given that they were exposed to a suspect rabid animal and did not receive PEP ranged from 1 × 10-10 to 0.55. Fifty public health officials out of a target sample size of 102 responded to the survey. Using logistic regression, a risk threshold was estimated for PEP recommendation of 0.0004; PEP may not be recommended for exposures with probabilities below this threshold. CONCLUSIONS AND RELEVANCE: In this modeling study of rabies in the US, the risk of death|exposure was quantified and a risk threshold was estimated. These results could be used to inform the decision-making process as to the appropriateness of recommending rabies PEP. |
Serial interval and incubation period estimates of monkeypox virus infection in 12 jurisdictions, United States, May-August 2022
Madewell ZJ , Charniga K , Masters NB , Asher J , Fahrenwald L , Still W , Chen J , Kipperman N , Bui D , Shea M , Saunders K , Saathoff-Huber L , Johnson S , Harbi K , Berns AL , Perez T , Gateley E , Spicknall IH , Nakazawa Y , Gift TL . Emerg Infect Dis 2023 29 (4) 818-821 Using data from 12 US health departments, we estimated mean serial interval for monkeypox virus infection to be 8.5 (95% credible interval 7.3-9.9) days for symptom onset, based on 57 case pairs. Mean estimated incubation period was 5.6 (95% credible interval 4.3-7.8) days for symptom onset, based on 35 case pairs. |
Modeling the impact of sexual networks in the transmission of monkeypox virus among gay, bisexual, and other men who have sex with men - United States, 2022
Spicknall IH , Pollock ED , Clay PA , Oster AM , Charniga K , Masters N , Nakazawa YJ , Rainisch G , Gundlapalli AV , Gift TL . MMWR Morb Mortal Wkly Rep 2022 71 (35) 1131-1135 What is already known about this topic? The 2022 monkeypox outbreak is associated with sexual and intimate contact. Survey data suggest that gay, bisexual, and other men who have sex with men (MSM), who have been disproportionately affected, are reducing one-time partnerships. What is added by this report? Modeling of sexual infection transmission between men indicates that one-time partnerships, which account for 3% of daily sexual partnerships and 16% of daily sex acts, account for approximately 50% of daily Monkeypox virus (MPXV) transmission. A 40% reduction in one-time partnerships might delay the spread of monkeypox and reduce the percentage of persons infected by 20% to 31%. What are the implications for public health practice? Reductions in one-time partnerships, already being reported by MSM, might significantly reduce MPXV transmission. © 2022 Department of Health and Human Services. All rights reserved. |
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