Tracing the start of COVID-19 in GA

At a time when COVID-19 appears to be receding in much of Georgia, it’s worth revisiting the start of the pandemic in early 2020. Emory virologist Anne Piantadosi and colleagues have a paper in Viral Evolution on the earliest SARS-CoV-2 genetic sequences detected in Georgia. Analyzing relationships between those virus sequences and samples from other states and countries can give us an idea about where the first COVID-19 infections in Georgia came from. We can draw Read more

Reddit as window into opioid withdrawal strategies

Drug abuse researchers are using the social media site Reddit as a window into the experiences of people living with opioid addiction. Abeed Sarker in Emory's Department of Biomedical Informatics has a paper in Clinical Toxicology focusing on the phenomenon of “precipitated withdrawal,” in collaboration with emergency medicine specialists from Penn, Rutgers and Mt Sinai. Precipitated withdrawal is a more intense form of withdrawal that can occur when someone who was using opioids starts medication-assisted treatment Read more

CROI: HIV cure report and ongoing research

The big news out of CROI (Conference on Retroviruses and Opportunistic Infections) was a report of a third person being cured of HIV infection, this time using umbilical cord blood for a hematopoetic stem cell transplant. Emory’s Carlos del Rio gave a nice overview of the achievement for NPR this morning. As del Rio explains, the field of HIV cure research took off over the last decade after Timothy Brown, known as “the Berlin patient,” Read more

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Tracing the start of COVID-19 in GA

At a time when COVID-19 appears to be receding in much of Georgia, it’s worth revisiting the start of the pandemic in early 2020. Emory virologist Anne Piantadosi and colleagues have a paper in Viral Evolution on the earliest SARS-CoV-2 genetic sequences detected in Georgia.

Analyzing relationships between those virus sequences and samples from other states and countries can give us an idea about where the first COVID-19 infections in Georgia came from. We can draw a few conclusions, such as: there was no “Patient Zero”, at least here.

According to sequence analysis in the paper, multiple early introductions of SARS-CoV-2 into Georgia occurred, probably coming from Asia, weeks before the first officially reported case in March 2020. The authors suggest that the early focus on returning international travelers was misplaced, as opposed to broader testing of patients with COVID-19 symptoms.

“SARS-CoV-2 was likely spreading within the state for approximately three weeks prior to detection in either diagnostic or sequencing data,” the authors write.

Tree showing relationships between SARS-CoV-2 genetic sequences from Georgia and other states/countries

In Georgia, the subclade, or swarm of related viruses, that was dominant early on (called 19B) disappeared by the end of April, eclipsed by variants carrying the D614G mutation. This was an early hint – even before the emergence of B117/Alpha and other variants such as Delta and Omicron — that SARS-CoV-2 would evolve through competition. 

Similarly, sequence analysis from Washington state – the site of the first COVID-19 case identified in the United States — has shown that the first official case did not lead directly to the initial wave of infections there. The first wave actually fizzled out as a result of public health interventions, but other undetected infections in Washington in February 2020 led to sustained downstream transmission. 

The co-first authors of the Viral Evolution paper are Emory infectious disease specialist Ahmed Babiker and graduate student Michael Martin, with co-authors from the Centers of Disease Control and Prevention. The paper analyzes sequences from Emory Healthcare patients along with previously available sequences.

In a few cases, scientists attempted to trace relationships between infected patients who had recently travelled to other countries (Italy, Switzerland) or other states (Louisiana, Colorado), but the available data did not confirm all of those connections. 

Keep in mind that SARS-CoV-2 testing was very limited at the start of the pandemic, because of short supplies as well as FDA policy. More extensive virus sequencing efforts at Emory did not begin until mid-March 2020. With respect to viruses, we only see what we look for, and scientists can’t analyze samples they don’t have. If more samples were available from January or February, what would we find? Also, this paper’s analysis does not include any (known) samples from a February 2020 funeral in Albany, GA that was considered a “super-spreader event.” 

Two years later, has SARS-CoV-2 genomic surveillance improved? Piantadosi says that her team’s paper should be viewed in combination with their recent paperon the detection of the first Omicron case in Georgia, a woman who became sick in November 2021 while visiting Cape Town, South Africa.

 “That’s an example of where we did better,” Piantadosi says. “It does speak to how much surveillance has improved. We were conducting routine surveillance – not focusing on returning travelers.”

In the Omicron case, the woman in question first went to a community testing site, and those samples were not available for sequence analysis.

Piantadosi says that “we’ve achieved Phase I” – in that large hospitals or health systems such as Emory are collecting SARS-CoV-2 sequences, and the state Department of Public Health and large diagnostic services companies are also doing so. But as more SARS-CoV-2 testing is performed at home – generally a good thing for convenience and public health — surveillance for new variants needs to continue, she says.

Posted on by Quinn Eastman in Uncategorized Leave a comment

Reddit as window into opioid withdrawal strategies

Drug abuse researchers are using the social media site Reddit as a window into the experiences of people living with opioid addiction.

Abeed Sarker in Emory’s Department of Biomedical Informatics has a paper in Clinical Toxicology focusing on the phenomenon of “precipitated withdrawal,” in collaboration with emergency medicine specialists from Penn, Rutgers and Mt Sinai.

Precipitated withdrawal is a more intense form of withdrawal that can occur when someone who was using opioids starts medication-assisted treatment with buprenorphine – and also when someone receives naloxone for an overdose.

Precipitated withdrawal is reported to occur more often when someone has a history of fentanyl use, possibly because fentanyl remains in the body’s peripheral tissues, even during periods of abstinence.

When it occurs prior to medication-assisted treatment, precipitated withdrawal is reported to occur more often when someone has a history of fentanyl use, possibly because fentanyl remains in the body’s peripheral tissues, even during periods of abstinence. The buprenorphine washes out remaining fentanyl or its relatives quickly, leading to symptoms such as diarrhea and vomiting, and sometimes to dehydration and hospitalization.

“From Reddit, we have found that people who use opioids had been talking about it [precipitated withdrawal] for a couple of years now and they have, as a community, come up with their own self-management strategies,” Sarker says.

The strategies are based on microdosing; one approach is called the “Bernese method.”

“These findings are important because this cohort is very difficult to follow, and therefore studying causes and solutions to precipitated withdrawal after buprenorphine initiation is challenging,” Sarker says. “We are essentially trying to give people who use opioids a voice.”

Read more

Posted on by Quinn Eastman in Neuro, Uncategorized Leave a comment

Poop substitute effective vs C. diff

A pill derived from human feces can effectively ward off Clostridium difficile diarrhea, according to the results of a clinical trial published in the New England Journal of Medicine.

Clinical microbiologist/infectious disease specialist Colleen Kraft and Emory patients contributed to the Phase III, 182 patient study, which was sponsored by Seres Therapeutics. Kraft is associate chief medical officer at Emory University Hospital and 2022 president-elect of the American Society for Microbiology.

Colleen Kraft, MD

Seres’ pill is an alternative to fecal microbiota transplant (FMT), a treatment for C.difficile that is both well-established and difficult to standardize. Everyone is intimately familiar with the material necessary for FMT, but its microbial components vary with the individual donor, diet and time. That presents some inconsistency and risk that has delayed FDA approval for the procedure.

Moving toward an “off the shelf” product, Seres takes stool from prescreened donors and treats the material with ethanol, killing some microbes and leaving behind bacterial spores that can compete for intestinal real estate with C. difficile. A previous study of Seres’ pill was unsuccessful, inspiring the headline “Sham poo washes out.” More information about the newer study and the company’s plans are in this Science article.

C. difficile colonization sometimes occurs after antibiotics deplete healthier forms of intestinal bacteria. Kraft and colleagues at Emory have been investigating whether FMT can prevent colonization by antibiotic-resistant bacteria in kidney transplant patients, who have (deliberately) dampened immune systems and need to take antibiotics.

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Diabetic foot ulcers: cell types identified that may contribute to healing

Diabetic foot ulcerations — open sores or wounds that refuse to heal – affect more than 15 percent of people with diabetes and result in thousands of lower extremity amputations per year in the United States.

To gain a better understanding of diabetic foot ulcers’ biology, a team of researchers at Emory and Beth Israel Deaconess Medical Center in Boston compared cells taken from patients with ulcers that healed to those taken from patients whose ulcers failed to heal, as well as to cells taken from intact forearm skin in patients with and without diabetes.

The team identified a subpopulation of fibroblasts enriched in the foot ulcers that healed, pointing to potential interventions. The results were published in Nature Communications on January 10.

“In this study, we present a comprehensive single cell map of the diabetic foot ulcer microenvironment,” says Manoj Bhasin, PhD, associate professor of pediatrics and biomedical informatics at Emory University School of Medicine, who is co-corresponding author of the study. “To our knowledge, we are the first to identify a unique subpopulation of fibroblasts that are significantly enriched in diabetic foot ulcers that are destined to heal.”

Various cell types, including endothelial cells, fibroblasts, keratinocytes and immune cells, were known to play an important role in wound healing processes. Yet diabetic foot ulcerations’ failure to heal and high associated mortality remain poorly understood.

“Our data suggests that specific fibroblast subtypes are key players in healing these ulcers and targeting these cells could be one therapeutic option,” says co-corresponding author Aristidis Veves, DSc, MD, director of the Rongxiang Xu, MD, Center for Regenerative Therapeutics and research director of the Joslin-Beth Israel Deaconess Foot Center. “While further testing is needed, our data set will be a valuable resource for diabetes, der