2023 New Year’s Letter from Prof. Marc Lipsitch, CCDD Director


Dear colleagues, alumni and friends,

New year’s greetings from the Center for Communicable Disease Dynamics (CCDD) at the Harvard Chan School. A lot has happened in the world of infectious diseases since I last wrote to you in Fall 2021, when I was beginning my temporary role as Director of Science for the Center for Forecasting and Outbreak Analytics (CFA) at CDC. More on that exciting work below.

In the last year and a bit, we’ve lived through the COVID-19 Omicron surge and its ongoing aftershocks and now a “tripledemic” of influenza, COVID-19, and respiratory syncytial virus (RSV) that continues to stress health care systems, especially pediatric ones, in some places. China’s abrupt reversal of its zero-COVID policy, without first increasing vaccine coverage and antiviral availability as recommended by experts, has led to infections and deaths on a scale that is undoubtedly large, but hard to estimate given simultaneous dramatic cuts in testing and opaque reporting. This puts well over a billion Chinese citizens at risk and creates an opportunity for the virus to further evolve to become more transmissible and resistant to the immunity developed through vaccines and prior infections.

The global outbreak of mpox (formerly known as monkeypox), while infecting close to 100,000 in over 100 countries, has fortunately receded before reaching the levels some had feared. Likewise, an Ebola outbreak in Uganda, also of great concern some weeks back, appears to have quieted. Cholera has resurged in Haiti. The list goes on, and this is just a sample of the new and reemerging outbreaks that augment the continuing tolls from causes like HIV, malaria, tuberculosis, and drug-resistant bacteria, which CCDD and many of our collaborators at Harvard continue to work on.

COVID-19 remains a focus of our research at CCDD, led by Profs. Bill Hanage, Yonatan Grad and myself:

  • Bill Hanage’s group continues to improve understanding of how wastewater and genome sequencing contribute to surveillance of COVID-19 and other infections. Together, we have used theoretical models to understand how SARS-CoV-2 variants continue to spread even as immunity builds within a population.
  • Yonatan Grad’s collaboration with the National Basketball Association, using testing data from the NBA’s “bubble” campus, continues to produce some of the world’s most detailed information on when, and how long, people are infectious with COVID-19. He is also working with state and local public health departments to leverage an exciting new approach developed at CCDD which improves our ability to detect disease trends when changing testing patterns mean less data available.
  • I’ve worked with colleagues at United Health to better understand the effects of long COVID in the 65+ population, and I continue collaborating with Israeli and Harvard scientists to study the impact of the Pfizer/BioNTech vaccine with different age groups, booster doses, and variants. This month, I’ll be visiting Israel to discuss further research ideas with my collaborators at Clalit Research Institute and Sheba Medical Center, and am honored to attend a dinner meeting with Israeli President Isaac Herzog about this work.

It’s recently been estimated that drug-resistant bacterial infections take more lives each year than HIV, tuberculosis, or malaria. Drug resistance and the broader challenge of how pathogens evolve in human populations was one of our main foci before COVID, and we are returning to this and other pressing questions. Key areas of our non-COVID work include:

  • understanding the drivers of antibiotic use in children, resistance related to increased seasonal use in winter, and transfer of resistance genes that allow bacteria to evade antibiotics.
  • applying new approaches (machine learning and phylogenomics) to improve testing for drug-resistant gonorrhea, one of the most common sexually transmitted diseases in the US.
  • restarting a long-term set of studies with Bill Hanage and numerous collaborators that are providing what may be the first predictive theory of bacterial evolution—essentially telling us if vaccination increases or decreases fitness of a disease strain.
  • reevaluating the value of HIV treatment-as-prevention in Africa using advanced genomic analyses.
  • understanding parasite dynamics to optimize drug trials for Chagas disease, which affects approximately 8 million people in Mexico, Central and South America, led by Prof. Caroline Buckee.


For me personally, this year has also been heavily invested in building the new Center for Forecasting and Outbreak Analytics (CFA) at CDC. When I last wrote, the work had just started, with a core team of five. I had agreed to work three-quarters time for an academic year as the Director for Science to get it off the ground. The work was so exciting, and so important, that I signed on for another year. I am now splitting my time evenly between CFA and CCDD. CFA’s staff has grown to nearly 30 full time modelers, science communicators, and managers. At full capacity, CFA will employ 130 experts to set a new course for public health data and analytics in the US. CFA began with $200 million in one-time funds from the American Rescue Plan. A major milestone was our first annual appropriation, $50 million in the Omnibus bill passed and signed in December. The CDC has been justly criticized for being slow to release data and to educate the public as health emergencies evolve, and I’m confident that this investment in CFA is worthwhile. Below are a few examples of how CFA has already improved decision making through better, faster data–and we are just getting started.

In late Fall 2021, the threat of the Omicron wave was fast approaching. Modeling done by colleagues within the Department of Health and Human Services with CFA collaboration showed that the wave would bring unprecedented numbers of cases, peaking in January 2022. But how severe would those cases be? CFA’s team of five, in collaboration with Kaiser Permanente in Southern California and CCDD alum Dr. Joe Lewnard (now faculty at UC Berkeley), answered that question in record time. We used routinely collected health data which showed definitively that those with Omicron infections were at substantially lower risk of severe outcomes relative to Delta infections, meaning that though the peak would stress health systems, it would not cause as much damage, per case, as Delta had. CDC Director Rochelle Walensky presented the first findings from this study at a White House press conference less than 40 days after we first conceived it. It provided a key evidence base for extending countermeasures while keeping schools, workplaces and other settings open. It also demonstrated how we could generate reliable data quickly in the US, and has served as a catalyst to extend that capacity at CFA and throughout CDC.

During July – October 2022, the CFA team produced four technical reports on mpox for the scientific community. These reports provided the situational awareness needed to understand the scope of the disease in the US and globally, dynamics of the US outbreak, and priority research areas to respond to this new public health threat. These reports were a direct result of the fact-finding trip my co-director, Dr. Dylan George, and I took to the UK, where we were struck by the exceptional quality and timeliness of similar reports issued by the UK Health Security Agency. We have shamelessly taken good ideas whatever their source, and technical reports like this are one of the key ways CDC will produce data and forecasts rapidly and regularly in the future.

CFA has also pushed CDC’s cloud computing infrastructure forward, developing and deploying a virtual analyst workstation. This allows CFA’s analysts to perform large-scale sophisticated computational analyses without constraint from computational power. Importantly, CFA is already supporting the use of this resource in other parts of CDC, with a goal of expanding availability to local health departments, academic institutions, and other partners.

All of this work directly supports CDC’s Moving Forward initiative, which aims to make public health information and guidance immediately available to the public. I believe that Dr. Walensky has a clear and accurate view of how CDC should orient its efforts to faster, better responses to health emergencies. I’m proud that as a new initiative at CDC, CFA has been able to help advance some of these efforts.


The last year or so has sharpened and clarified my sense of responsibility for training the next generation of public health leaders. We’ll be redoubling our efforts and seeking philanthropic support to train those who will be positive disruptors in public health.

A hallmark of CCDD’s approach in training postdocs and students is to equip them with a range of skills that allow them to tackle scientific and public health problems with the most effective tools, not just the ones they happen to have learned. In my role at CDC, I’ve watched several of these trainees in action. Some of the highlights include:

  • Seeing Dr. Rebecca Kahn take on a role as Senior Scientist at CFA, moving skillfully from research on waning vaccine effectiveness, to scoping out CFA’s data needs, shepherding the release of one of our mpox technical reports, and starting her training in CDC’s prestigious Epidemic Intelligence Service (EIS) program. In her “spare time” she was also leading a study on ethics related to antimicrobial resistance, mentoring a master’s student, and consulting on vaccine study design for the Pan-American Health Organization.
  • Working with Dr. Joe Lewnard of UC Berkeley on COVID-19 collaboratively with CDC, and appreciating his exceptional capacity to analyze data with both care and speed to get important answers about Omicron severity (as described above) and on other projects. Joe did his PhD at Yale supervised by faculty who are CCDD alumni, and his postdoc at CCDD.
  • Hearing from Dr. Anne Zink, Chief Health Officer of the State of Alaska, about the key role that Dr. Eric Mooring, a CCDD alum, played in that state’s pandemic response.
  • Admiring the speed with which, after joining the EIS, CCDD alumni Drs. Emma Accorsi and Kevin Ma were placed in the lead for important studies of COVID-19 vaccine effectiveness and pediatric viral diseases.

Seeing the difference these trainees can make in a crisis is the best motivation I could ask for to return my full energy to leading CCDD after this academic year, so we can continue to produce such exceptional graduates.

Wishing you a happy and healthy new year.



Marc Lipsitch, DPhil
Professor of Epidemiology
Director, Center for Communicable Disease Dynamics
Harvard T.H. Chan School of Public Health

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