CCDD
@ccdd-hsph.bsky.social
Center for Communicable Disease Dynamics. Research on mathematical modeling of Infectious Diseases.
Funded opportunities for students/researchers from under-represented groups.
Funded opportunities for students/researchers from under-represented groups.
Reposted by CCDD
New preprint: with increasing resistance to ceftriaxone, the last recommended antibiotic for gonorrhea, we urgently need new drugs. Two--zoliflodacin & gepotdiacin--are up for approval by the FDA in Dec. Here we show a point mutation can result in cross-resistance. www.biorxiv.org/content/10.1...
Zoliflodacin and gepotidacin cross-resistance in Neisseria gonorrhoeae
Resistance to zoliflodacin, a first-in-class antibiotic for gonorrhea treatment, can occur through gyrBD429N, but this mutation's impact on fitness and resistance to other topoisomerase targeting drug...
www.biorxiv.org
November 26, 2025 at 2:39 AM
New preprint: with increasing resistance to ceftriaxone, the last recommended antibiotic for gonorrhea, we urgently need new drugs. Two--zoliflodacin & gepotdiacin--are up for approval by the FDA in Dec. Here we show a point mutation can result in cross-resistance. www.biorxiv.org/content/10.1...
Reposted by CCDD
Now out in @natcomms.nature.com Kudos to @tylim.bsky.social and @jameshay.bsky.social for a huge effort and thanks to all the collaborators for their hard work. See the final version here: www.nature.com/articles/s41...
November 20, 2025 at 9:58 PM
Now out in @natcomms.nature.com Kudos to @tylim.bsky.social and @jameshay.bsky.social for a huge effort and thanks to all the collaborators for their hard work. See the final version here: www.nature.com/articles/s41...
Experimental mRNA flu vaccine is more effective than conventional flu shot, but causes more side effects. @billhanage.bsky.social weighs in at @cidrap.bsky.social. Read it here at bit.ly/4o8qIo0
Experimental mRNA flu vaccine is more effective than conventional flu shot, but causes more side effects
bit.ly
November 21, 2025 at 7:03 PM
Experimental mRNA flu vaccine is more effective than conventional flu shot, but causes more side effects. @billhanage.bsky.social weighs in at @cidrap.bsky.social. Read it here at bit.ly/4o8qIo0
New study shows that shifts in SARS‑CoV‑2 Ct value distributions can help nowcast epidemic trends, revealing both strong potential and key real‑world limitations for Ct‑based surveillance. From CCDD alumni TY Lim & @jameshay.bsky.social and faculty @yhgrad.bsky.social at bit.ly/4o37EaN
Nowcasting epidemic trends using hospital- and community-based virologic test data - Nature Communications
Population-level distributions of SARS-CoV-2 viral load can correlate with epidemic trends. Here, the authors use viral loads to nowcast epidemic growth rates over two-week periods and investigate how...
bit.ly
November 21, 2025 at 3:54 PM
New study shows that shifts in SARS‑CoV‑2 Ct value distributions can help nowcast epidemic trends, revealing both strong potential and key real‑world limitations for Ct‑based surveillance. From CCDD alumni TY Lim & @jameshay.bsky.social and faculty @yhgrad.bsky.social at bit.ly/4o37EaN
A modeling study led by @pantbinod.bsky.social, a CCDD-affiliated postdoc in MIGHTE LAB, Northeastern University, shows fungal biocontrol could reduce malaria-carrying mosquitoes by up to 90%—full story at Northeastern Global News bit.ly/3LDJma1
Want to eradicate malaria-bearing mosquitoes? Try fungus, this researcher says
A Northeastern postdoc has created a mathematical model that demonstrates how a fungal solution could control malarial mosquito populations.
bit.ly
November 14, 2025 at 8:54 PM
A modeling study led by @pantbinod.bsky.social, a CCDD-affiliated postdoc in MIGHTE LAB, Northeastern University, shows fungal biocontrol could reduce malaria-carrying mosquitoes by up to 90%—full story at Northeastern Global News bit.ly/3LDJma1
New method for approximate Bayesian inference in extended latent Gaussian models uses adaptive Gauss-Hermite quadrature—improves accuracy & speed, demonstrated on small-area model for district-level epidemic estimates in Malawi. From authors incl CCDD’s @jeff-imai-eaton.bsky.social @ bit.ly/4oLH7QA
Fast approximate Bayesian inference of HIV indicators using PCA adaptive Gauss-Hermite quadrature
Naomi is a spatial evidence synthesis model used to produce district-level HIV epidemic indicators in sub-Saharan Africa. Multiple outcomes of policy …
bit.ly
November 14, 2025 at 5:24 PM
New method for approximate Bayesian inference in extended latent Gaussian models uses adaptive Gauss-Hermite quadrature—improves accuracy & speed, demonstrated on small-area model for district-level epidemic estimates in Malawi. From authors incl CCDD’s @jeff-imai-eaton.bsky.social @ bit.ly/4oLH7QA
Reporting on calibration methods in infectious disease models is inconsistent—our new PIPO framework & scoping review reveal gaps and offer guidance to boost transparency and reproducibility. Read more from CCDD authors Emmanuelle Dankwa, Léa Cavalli, @ruchitabalasub1.bsky.social @ bit.ly/4hPBw9g
Calibration of transmission-dynamic infectious disease models: A scoping review and reporting framework
Author summary Calibration, the identification of parameter values so that model outcomes are consistent with observed data or other evidence, is often employed in the process of obtaining model resul...
bit.ly
November 7, 2025 at 3:04 PM
Reporting on calibration methods in infectious disease models is inconsistent—our new PIPO framework & scoping review reveal gaps and offer guidance to boost transparency and reproducibility. Read more from CCDD authors Emmanuelle Dankwa, Léa Cavalli, @ruchitabalasub1.bsky.social @ bit.ly/4hPBw9g
New paper from Mozambique Instituto Nacional de Saúde and collaborators including CCDD’s @jeff-imai-eaton.bsky.social on findings from the INSIDA 2021 household survey—highlighting heterogeneous epidemic burden across districts and high burden in coastal port cities. bit.ly/47QFBpg
<em>Journal of the International AIDS Society</em> | IAS HIV Research Journal | Wiley Online Library
Introduction Accurate information is needed to prioritize programmes and resources that address gaps in the HIV response. We examined findings from the 2021 Mozambique Population-based HIV Impact As...
bit.ly
November 6, 2025 at 3:24 PM
New paper from Mozambique Instituto Nacional de Saúde and collaborators including CCDD’s @jeff-imai-eaton.bsky.social on findings from the INSIDA 2021 household survey—highlighting heterogeneous epidemic burden across districts and high burden in coastal port cities. bit.ly/47QFBpg
New study led by Salome Kuchukhidze, @mintturonn.bsky.social & @jeff-imai-eaton.bsky.social finds that over 1 in 4 US women living w/ HIV reported past-year intimate partner violence, with pregnant women at a particularly high risk. bit.ly/47YX2F2
bit.ly
November 5, 2025 at 3:35 PM
New study led by Salome Kuchukhidze, @mintturonn.bsky.social & @jeff-imai-eaton.bsky.social finds that over 1 in 4 US women living w/ HIV reported past-year intimate partner violence, with pregnant women at a particularly high risk. bit.ly/47YX2F2
Antimicrobial treatments affect both patients and those around them—these indirect effects matter. In our new paper, Juan Gago, @cboyer.bsky.social, and @mlipsitch.bsky.social present a causal framework to estimate them. Read more at bit.ly/4oRc99e
bit.ly
November 4, 2025 at 3:13 PM
Antimicrobial treatments affect both patients and those around them—these indirect effects matter. In our new paper, Juan Gago, @cboyer.bsky.social, and @mlipsitch.bsky.social present a causal framework to estimate them. Read more at bit.ly/4oRc99e
New publication from @rumpl-er.bsky.social and @mlipsitch.bsky.social identify eight considerations to consider when including equity in future vaccine allocation models. Read them here at bit.ly/4nz8ZqC
Equity considerations in COVID-19 vaccine allocation modelling: a methodological study | Interface Focus
We conducted a methodological study of COVID-19 vaccine allocation modelling papers,
specifically looking for publications that considered equity. We found that most models
did not take equity into ac...
bit.ly
October 2, 2025 at 4:53 PM
New publication from @rumpl-er.bsky.social and @mlipsitch.bsky.social identify eight considerations to consider when including equity in future vaccine allocation models. Read them here at bit.ly/4nz8ZqC
Reposted by CCDD
“It’s hard to explain how the Secretary can think that the President deserves the Nobel Peace Prize for this, while at the same time believing that these vaccines are the most harmful that have ever been made”
Me on mRNA vaccines
hsph.harvard.edu/news/slashin...
Me on mRNA vaccines
hsph.harvard.edu/news/slashin...
Slashing of funding for mRNA vaccine development raises concern | Harvard T.H. Chan School of Public Health
In August, the U.S. Department of Health and Human Services (HHS) cancelled nearly $500 million in contracts that funded mRNA vaccine development. The mRNA
hsph.harvard.edu
September 26, 2025 at 1:05 PM
“It’s hard to explain how the Secretary can think that the President deserves the Nobel Peace Prize for this, while at the same time believing that these vaccines are the most harmful that have ever been made”
Me on mRNA vaccines
hsph.harvard.edu/news/slashin...
Me on mRNA vaccines
hsph.harvard.edu/news/slashin...
Mauricio Santillana and his team at Northeastern leveraged machine learning as a "team member" to predict dengue fever outbreaks three months in advance with 80% accuracy—turning years of manual data crunching into overnight results. Read it here at bit.ly/4n2wkk9
How to use AI: Mauricio Santillana gave an algorithm accurate models to analyze data
Mauricio Santillana tested models that foretell upsurges of the disease in 180 locations around the world.
bit.ly
September 17, 2025 at 3:03 PM
Mauricio Santillana and his team at Northeastern leveraged machine learning as a "team member" to predict dengue fever outbreaks three months in advance with 80% accuracy—turning years of manual data crunching into overnight results. Read it here at bit.ly/4n2wkk9
New modeling from Nick Menzies, @jeff-imai-eaton.bsky.social, @tedhcohen.bsky.social, and collaborators, shows that health aid cuts could lead to over 1.5 million more childhood TB deaths in LMICs by 2034. Read more at bit.ly/47HsoR2
Potential paediatric tuberculosis incidence and deaths resulting from interruption in programmes supported by international health aid, 2025–34: a mathematical modelling study
Without actions to restore discontinued services, cuts to health aid for tuberculosis
and HIV programmes could result in millions of additional childhood tuberculosis cases
and deaths in low-income an...
bit.ly
September 16, 2025 at 7:17 PM
New modeling from Nick Menzies, @jeff-imai-eaton.bsky.social, @tedhcohen.bsky.social, and collaborators, shows that health aid cuts could lead to over 1.5 million more childhood TB deaths in LMICs by 2034. Read more at bit.ly/47HsoR2
New research highlighting key barriers and opportunities for targeted interventions to enhance motivation, access, and use of HIV prevention among young people in Zimbabwe. Read more from the Manicaland Centre for Public Health Research including @jeff-imai-eaton.bsky.social bit.ly/3Kcznri
Measurement and interpretation of the Harare HIV combination prevention cascade in priority populations: a population survey of adolescent girls and young women and young men in Zimbabwe
Introduction HIV-negative adolescent girls and young women (AGYW), and men (ABYM), have disproportionately high HIV incidence in many African countries. We used a new HIV Prevention Cascade (HPC) appr...
bit.ly
September 9, 2025 at 2:56 PM
New research highlighting key barriers and opportunities for targeted interventions to enhance motivation, access, and use of HIV prevention among young people in Zimbabwe. Read more from the Manicaland Centre for Public Health Research including @jeff-imai-eaton.bsky.social bit.ly/3Kcznri
Reposted by CCDD
New preprint reporting a large piece of work by Katherine Jia to define estimands and estimators for direct impact of vaccines with arbitrary rollout schedules arxiv.org/abs/2509.05508
with Alyssa Bilinski, @chrisboyer.bsky.social and me
with Alyssa Bilinski, @chrisboyer.bsky.social and me
Defining and Estimating Outcomes Directly Averted by a Vaccination Program when Rollout Occurs Over Time
During the COVID-19 pandemic, estimating the total deaths averted by vaccination has been of great public health interest. Instead of estimating total deaths averted by vaccination among both vaccinat...
arxiv.org
September 9, 2025 at 12:12 PM
New preprint reporting a large piece of work by Katherine Jia to define estimands and estimators for direct impact of vaccines with arbitrary rollout schedules arxiv.org/abs/2509.05508
with Alyssa Bilinski, @chrisboyer.bsky.social and me
with Alyssa Bilinski, @chrisboyer.bsky.social and me
Reposted by CCDD
Join us tomorrow, September 10, at 1 pm ET, for a @hsphniehsctr.bsky.social and @harvardenvhealth.bsky.social seminar with Dr. Caroline Buckee of @harvardepi.bsky.social. In-person and virtual! Visit hsph.me/niehs-seminar for more info and Zoom registration.
September 9, 2025 at 12:36 PM
Join us tomorrow, September 10, at 1 pm ET, for a @hsphniehsctr.bsky.social and @harvardenvhealth.bsky.social seminar with Dr. Caroline Buckee of @harvardepi.bsky.social. In-person and virtual! Visit hsph.me/niehs-seminar for more info and Zoom registration.
“I think of antibiotics as infrastructure” @yhgrad.bsky.social interviewed for the Harvard Gazette, 'Racing against antibiotic resistance'. Read it here at bit.ly/47PdOqv
Racing against antibiotic resistance — Harvard Gazette
Scientists fear funding cuts will slow momentum in their war with evolving bacteria— one of America’s most urgent healthcare problems.
bit.ly
August 28, 2025 at 4:12 PM
“I think of antibiotics as infrastructure” @yhgrad.bsky.social interviewed for the Harvard Gazette, 'Racing against antibiotic resistance'. Read it here at bit.ly/47PdOqv
Reposted by CCDD
Very pleased to share this newly published work with Aishani Aatresh, part of her exceptional Harvard undergrad thesis. journals.asm.org/doi/10.1128/... .
What is the relationship between viral prospecting in animals and medical countermeasure development? | mBio
Sampling in animal populations to detect novel viruses before they infect humans has
been a major activity justified by several considerations, notably by the idea that
finding such viruses will stimu...
journals.asm.org
August 25, 2025 at 7:43 PM
Very pleased to share this newly published work with Aishani Aatresh, part of her exceptional Harvard undergrad thesis. journals.asm.org/doi/10.1128/... .
Mauricio Santillana and his team at Northeastern have developed a machine learning method that predicts dengue fever outbreaks with 80% accuracy, equipping public health officials with a powerful new tool to prepare for surges. Read it here at bit.ly/4my3DLM
Researchers use machine learning to predict dengue fever with 80% accuracy
Northeastern researchers use machine learning to predict dengue fever outbreaks, giving health officials time to prepare for spikes.
bit.ly
August 22, 2025 at 8:08 PM
Mauricio Santillana and his team at Northeastern have developed a machine learning method that predicts dengue fever outbreaks with 80% accuracy, equipping public health officials with a powerful new tool to prepare for surges. Read it here at bit.ly/4my3DLM
Multi-country analysis of HIV household surveys identifies large geographic & education disparities in HIV prevalence & engagement w/ HIV prevention and treatment services. Read from Adrien Allorant, @mat-mg.bsky.social, & colleagues including CCDD’s @jeff-imai-eaton.bsky.social @ bit.ly/45CZajA
<em>Journal of the International AIDS Society</em> | IAS HIV Research Journal | Wiley Online Library
Introduction
Socio-demographic and geographic disparities in HIV prevalence, uptake of HIV testing and access to antiretroviral therapy (ART) persist in high HIV burden countries. Understanding demo.....
bit.ly
August 19, 2025 at 1:30 PM
Multi-country analysis of HIV household surveys identifies large geographic & education disparities in HIV prevalence & engagement w/ HIV prevention and treatment services. Read from Adrien Allorant, @mat-mg.bsky.social, & colleagues including CCDD’s @jeff-imai-eaton.bsky.social @ bit.ly/45CZajA
AI-designed new antibiotics take on drug-resistant gonorrhea and MRSA—breaking into unexplored chemical territory and showing promise in mouse models. Led by colleagues at MIT, with contributions from @yhgrad.bsky.social. Read more at bit.ly/4mP1OK5
A generative deep learning approach to de novo antibiotic design
The antimicrobial resistance crisis necessitates structurally distinct antibiotics. While deep learning approaches can identify antibacterial compound…
bit.ly
August 18, 2025 at 6:21 PM
AI-designed new antibiotics take on drug-resistant gonorrhea and MRSA—breaking into unexplored chemical territory and showing promise in mouse models. Led by colleagues at MIT, with contributions from @yhgrad.bsky.social. Read more at bit.ly/4mP1OK5
Ensemble modeling combining mechanistic, statistical, and machine learning approaches improves province-level dengue forecasts worldwide, helping public health decision-makers allocate resources more effectively. Read more from Santillana Lab and collaborators at bit.ly/4luKGs6
Ensemble approaches for short-term dengue fever forecasts: A global evaluation study | PNAS
Dengue fever, a tropical vector-borne disease, is a leading cause of hospitalization
and death in many parts of the world, especially in Asia and L...
bit.ly
August 14, 2025 at 4:15 PM
Ensemble modeling combining mechanistic, statistical, and machine learning approaches improves province-level dengue forecasts worldwide, helping public health decision-makers allocate resources more effectively. Read more from Santillana Lab and collaborators at bit.ly/4luKGs6
Reposted by CCDD
And it is quite a paper!!! Really proud to have been a small part of this. I learned a *lot* about both plague and ancient DNA. Kudos to all involved!
First paper of the Key lab is out! We present the first prehistoric Y. pestis genome from a domesticated animal - a sheep - providing evidence that domestication elevated human infection risk with plague thousands of years ago. authors.elsevier.com/sd/article/S...
ScienceDirect.com | Science, health and medical journals, full text articles and books.
authors.elsevier.com
August 12, 2025 at 10:39 AM
And it is quite a paper!!! Really proud to have been a small part of this. I learned a *lot* about both plague and ancient DNA. Kudos to all involved!
New meta-analysis updates global estimates of perinatal & breastfeeding HIV transmission & effectiveness of prevention strategies. Findings inform new UNAIDS 2025 Epidemic Estimates - aidsinfo.unaids.org. From @mkwalters3.bsky.social, @jeff-imai-eaton.bsky.social & collaborators @ bit.ly/46BpIUw
AIDSinfo | UNAIDS
UNAIDS leads the world's most extensive data collection on HIV epidemiology, programme coverage and finance and publishes the most authoritative and up-to-date information on the HIV epidemic.
aidsinfo.unaids.org
August 4, 2025 at 3:06 PM
New meta-analysis updates global estimates of perinatal & breastfeeding HIV transmission & effectiveness of prevention strategies. Findings inform new UNAIDS 2025 Epidemic Estimates - aidsinfo.unaids.org. From @mkwalters3.bsky.social, @jeff-imai-eaton.bsky.social & collaborators @ bit.ly/46BpIUw