Virus World

NIH-funded study confirms white blood cell subtype as HIV reservoir, suggests new target for cure efforts. A subset of white blood cells, known as myeloid cells, can harbor HIV in people who have been virally suppressed for years on antiretroviral therapy, according to findings from a small study supported by the National Institutes of Health. In the study, researchers used a new quantitative method to show that HIV in specific myeloid cells—short-lived monocytes and longer-lived monocyte-derived macrophages—can be reactivated and infect new cells. The findings, published in Nature Microbiology(link is external), suggest that myeloid cells contribute to a long-lived HIV reservoir, making these cells an important but overlooked target in efforts to eradicate HIV. “Our findings challenge the prevailing narrative that monocytes are too short-lived to be important in cure efforts,” said study author Rebecca Veenhuis, Ph.D.(link is external), an assistant professor of molecular and comparative pathobiology and of neurology at Johns Hopkins University School of Medicine, Baltimore. “Yes, the cells are short-lived, but our follow-up data show that HIV can persist in monocytes over several years in people who are virally suppressed. The fact that we can detect HIV in these cells over such a long period suggests something is keeping the myeloid reservoir going.” The study, led by Veenhuis and colleagues at Johns Hopkins University School of Medicine, was supported by the National Institute of Mental Health, the National Institute of Allergy and Infectious Diseases, and the National Institute on Drug Abuse, all part of NIH. Antiretroviral medications are effective in treating HIV because they prevent the virus from infecting new cells and multiplying. However, HIV may still exist in cells that are in a resting, or latent, state, creating an HIV reservoir. CD4 T cells, a type of white blood cell, are the most well-studied HIV reservoir. Identifying HIV reservoirs is critical to cure efforts, as latent HIV can be reactivated if people stop taking antiretroviral medications. Monocytes are immune cells that circulate in the blood for about 3 days before traveling to tissue in various parts of the body, including the brain, where they can mature into macrophages. To date, it has not been clear whether latent HIV in these cells can become active again and infect other cells. “What’s really important in the long run is understanding how monocytes contribute to the tissue macrophage reservoir,” explained Janice Clements, Ph.D.(link is external), senior author on the study and professor of molecular and comparative pathobiology at Johns Hopkins University School of Medicine. “If monocytes can carry virus to the brain, or lung, or another part of the body and infect resident macrophages that are self-renewing and live almost indefinitely, that’s a real problem.”  

In the study, Veenhuis, Clements, and colleagues first measured HIV DNA in myeloid cells in a sample of 30 participants with HIV, all of whom were virally suppressed and had been on antiretroviral therapy for at least 5 years. They found detectable levels of HIV genetic material in monocytes and macrophages, though the levels were much lower than those observed in CD4 T cells. In some participants, the HIV genetic material found in monocytes was intact, which suggests it may be capable of infecting other cells if reactivated. They then used the new quantitative method they developed to directly measure viral spread from HIV found in myeloid cells. The researchers isolated monocytes from blood samples taken from 10 participants and nurtured the monocytes in cultures that contained antiretroviral drugs, to replicate the participants’ baseline physical state. After the monocytes differentiated into macrophages, the researchers introduced an immune activating agent and then added fresh white bloods cells to allow for the virus to spread to new cells. The researchers collected samples from the cell cultures several times over the next 12 days. They included checkpoints throughout the process to ensure that infected CD4 T cells did not interfere with their measurements. The results showed that cultures from five of the 10 participants had detectable HIV genetic material in monocyte-derived macrophages that could be reactivated to infect other cells and produce more virus. The participants who had these reactivatable reservoirs of HIV in monocyte-derived macrophages had higher overall levels of HIV DNA material.   Follow-up data from three participants showed that this reservoir can be long-lived, harboring latent HIV for months to several years. These reservoirs were stable and could be reactivated over time, indicating that monocyte-derived macrophages could contribute to viral rebound if antiretroviral treatment is disrupted. The researchers note that this study is small and larger studies with more diverse participant pools will be essential to accurately estimate the proportion of people who have latent HIV in myeloid cells. Investigating the mechanisms that replenish the monocyte reservoir over time is a critical next step in this research. “These findings underscore the importance of broadening the scope of HIV cure efforts,” said Joshua A. Gordon, M.D., Ph.D., director of the National Institute of Mental Health. “Shifting away from a sole focus on CD4 T cells to thinking about CD 4 T cells and myeloid cells together, in context, will propel the field toward more promising strategies for eradicating HIV.”

Published in:

 https://doi.org/10.1038/s41564-023-01349-3 

Significance

There is a risk that monkeypox could become endemic in Europe if the current outbreak isn’t brought under control and the virus spills back into susceptible animal species, the European Centre for Disease Prevention and Control said Monday  as it issued a risk assessment of the unprecedented event. The health agency said that if person-to-person transmission continues and if the monkeypox virus were to make its way into animal species in the region, it could become entrenched, though it suggested the risk is thought to be “very low.” “Currently, little is known about the suitability of European peri-domestic (mammalian) animal species to serve as a host for monkeypox virus,” the risk assessment stated, noting that rodents and squirrels are likely to be suitable hosts for the virus and transmission from people to pets is theoretically possible. “Such a spill-over event could potentially lead to the virus establishing in European wildlife and the disease becoming an endemic zoonosis.”  The agency noted that after a 2003 outbreak in the United States, public health authorities in this country did extensive surveillance looking for instances where the virus might have made its way into animals. But they found no evidence it had happened. The 2003 outbreak was traced back to infected small mammals imported from Ghana as pets — two rope squirrels, a Gambian rat, and three dormice. The animals infected nearby prairie dogs at a wholesale pet store and the prairie dogs infected 47 people in six states. As of yet, the virus is considered endemic only in a dozen countries in West and Central Africa, where human infections occur sporadically. Prior to this year, there have been only a few exported cases of monkeypox detected outside of the endemic countries — in the United States, the United Kingdom, Israel, and Singapore.

The natural reservoir — the animal or animals that are the source of the virus — is not known. “If human-to-animal transmission occurs, and the virus spreads in an animal population, there is a risk that the disease could become endemic in Europe,” the ECDC said in a statement. “As such, there needs to be a close intersectoral collaboration between human and veterinary public health authorities to manage exposed pets and prevent the disease from being transmitted to wildlife.” The number of cases in the current outbreak is changing rapidly as countries search for cases. Maria Van Kerkhove, who leads the emerging diseases and zoonoses unit in the World Health Organization’s Health Emergencies Program, said Monday that to date there are fewer than 200 confirmed and suspected cases. Eleven countries in Europe, as well as the United States, Canada, Israel, and Australia have reported confirmed cases. The virus currently appears to be spreading among men who have sex with men, though Van Kerkhove warned that surveillance is currently focused on finding cases through sexual health clinics. Casting a broader net will likely bring other cases to light, she and others have said.  Monkeypox is a pox virus and is related to the variola virus, which caused smallpox. That once dreaded disease was declared eradicated in 1980. The symptoms of monkeypox are similar to but milder than smallpox. Infected people develop flu-like symptoms — fever, body aches, chills — but also swollen lymph nodes. With one to three days of the onset of fever, a distinctive rash appears, often starting on the face.

Many conditions can cause rashes, but the monkeypox rash has some unusual features, notably the fact that vesicles can form on the palms of the hands. In this outbreak, a number of people have reported having had lesions on their genitals. In countries where it is endemic, the virus is believed to mainly spread to people from infected animals when people kill or prepare bushmeat for consumption.  Monkeypox is a pox virus and is related to the variola virus, which caused smallpox. That once dreaded disease was declared eradicated in 1980. The symptoms of monkeypox are similar to but milder than smallpox. Infected people develop flu-like symptoms — fever, body aches, chills — but also swollen lymph nodes. With one to three days of the onset of fever, a distinctive rash appears, often starting on the face. Many conditions can cause rashes, but the monkeypox rash has some unusual features, notably the fact that vesicles can form on the palms of the hands. In this outbreak, a number of people have reported having had lesions on their genitals. In countries where it is endemic, the virus is believed to mainly spread to people from infected animals when people kill or prepare bushmeat for consumption.

The origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing the global coronavirus disease 19 (COVID-19) pandemic, remains a mystery. Current evidence suggests a likely spillover into humans from an animal reservoir. Understanding the host range and identifying animal species that are susceptible to SARS-CoV-2 infection may help to elucidate the origin of the virus and the mechanisms underlying cross-species transmission to humans.

Here we demonstrated that white-tailed deer (Odocoileus virginianus), an animal species in which the angiotensin converting enzyme 2 (ACE2) - the SARS-CoV-2 receptor - shares a high degree of similarity to humans, are highly susceptible to infection. Intranasal inoculation of deer fawns with SARS-CoV-2 resulted in established subclinical viral infection and shedding of infectious virus in nasal secretions. Notably, infected animals(Jan. 14, 2021 transmitted the virus to non-inoculated contact deer. Viral RNA was detected in multiple tissues 21 days post-inoculation (pi). All inoculated and indirect contact animals seroconverted and developed neutralizing antibodies as early as day 7 pi. The work provides important insights into the animal host range of SARS-CoV-2 and identifies white-tailed deer as a susceptible wild animal species to the virus.

Preprint available in bioRxiv (Jan. 14, 2021):

https://doi.org/10.1101/2021.01.13.426628

For the first time in humans, a research team has shown that, as early as the first days of infection, HIV is able to create reservoirs where it will hide and persist during antiretroviral therapy. Until now, the scientific community did not know exactly when or how these viral reservoirs—the existence of which is a major obstacle to curing HIV—are established in human beings. In a study published in the journal Immunity, scientists led by Nicolas Chomont, a researcher at the CHUM Research Centre (CRCHUM) and professor at Université de Montréal, found that a small fraction of the virus integrates into the genome of CD4+ T cells in the very first weeks of infection (the acute phase), but does not replicate there. It therefore escapes the notice of the fastest diagnostic tool to date, which detects active viral replication.

CD4+ T cells are HIV's primary targets. They are white blood cells responsible for activating the human body's defense against infections. "With the help of an analysis technique developed in our laboratory, we were able to observe and count the T cells infected by the virus in human samples collected in the earliest stages of the infection," said Chomont, the study's principal author. "We succeeded in detecting the presence of the virus through sequencing even when it was hidden in cells that weren't participating in viral replication." To study these initial phases of the spread of the virus, Pierre Gantner, a former postdoctoral student in Chomont's lab and the study's first author, had access to samples of blood and inguinal lymph node tissue from 25 people in the first acute-infection cohort of the U.S. Military HIV Research Program in Thailand. This cohort, RV254/SEARCH010, was launched more than 10 years ago in collaboration with the Thai Red Cross AIDS Research Centre and has enrolled nearly 800 volunteers. Chomont and his team have been closely cooperating with their colleagues in Thailand since its launch.

Mapping the types of infected cells

Through their analysis technique, the CRCHUM scientists succeeded in counting the CD4+ T cells infected by the virus during the acute phase of the infection. These infected cells increased in number from 10 to 1,000 per million CD4+ T cells in less than seven days, thereby showing the extreme speed with which HIV spreads. The scientists also observed that the characteristics of the cells targeted by HIV in the first weeks of the infection varied quickly and differed depending on whether they were located in the blood or lymph nodes. "For example, we noticed that few Tfh—T follicular helper cells—are infected by the virus during the acute phase of the infection," said Chomont. "Since they play a crucial role in viral replication, the scientific community thought that they were the first to be infected." "In fact, we counted a lot more [infected Tfh] during the chronic phase of the disease, which is about two months after infection. At that point, they are actively contributing to the development of the disease." Until now, these types of studies have been carried out on animal models. Therefore, this is the first time that the early stages of the infection in humans have been described so precisely.

Destabilizing the reservoirs

A large part of global research dedicated to the study of HIV focuses on how to reactivate the virus lying dormant in the reservoirs in order to neutralize it. "'The earlier we start antiretroviral therapy, the more we prevent the virus from replicating and the more we limit the size of the reservoirs. We proved that in 2020," said Chomont. "However, it seems clear that early antiretroviral therapy should be combined with another treatment to force the virus out of its hiding places, because at the time of diagnosis latent reservoirs will have already been established in people infected with HIV." In collaboration with scientists from the United States, Chomont's research team is currently evaluating whether this type of treatment administered in the acute infection phase would prevent the establishment of viral reservoirs.

Cited study published (Feb. 17, 2023) in Immunity:

https://doi.org/10.1016/j.immuni.2023.01.030

The virus that causes COVID-19 is a prolific sack of genes that targets not just humans but nonhuman animals as well. And just as humans and animals can infect one another, animals can also infect other animals, says Amélie Desvars-Larrive, an epidemiologist at the University of Veterinary Medicine in Vienna. Scientists have learned a lot about how COVID spreads in humans but less about how it spreads between animals. To make it easier to study the connections among humans, animals and the virus, Desvars-Larrive and a team of researchers gathered scattered reports of COVID-infected mammals from all over the world to create a public database. Understanding how the virus spreads between nonhuman mammals, and then between those mammals and humans, can help us better manage the current pandemic—and prepare for the next one.

“We can’t continue to focus on humans, to have an anthropocentric point of view on this pandemic,” Desvars-Larrive says.  COVID has proved highly contagious among many mammal species: Infections have run rampant among captive mink, and fur farmers have had to kill their entire stocks to stop it. Deer appear particularly susceptible to the virus. Many cat species, both big and small, seem to get it as well. Barbara Han, a disease ecologist at the Cary Institute of Ecosystem Studies in Millbrook, N.Y., who was not involved in the database project, says having this kind of information in one place—rather than split among multiple sources managed by different organizations and government agencies—will likely make it faster and easier for her team to predict how the virus behaves. The database is growing as more animals are tested and reports shared, and scientists hope it will help them to track animal-to-animal COVID infections as well as transmission between animals and humans. Han says that beyond just tallying individual infected species, the database will make it easier for scientists to study how the COVID-causing SARS-CoV-2 virus affects mammal communities and entire ecosystems. “People are fascinated that this pathogen is now in [so many] animals and what it might mean for us,” Han says. “If we don’t have good information about which animals have it now, we can’t get those answers.”

Database at https://vis.csh.ac.at/sars-ani/ 

Scientists are studying whether long COVID could be linked to viral fragments found in the body months after initial infection.  In the chaos of the first months of the coronavirus pandemic, oncologist and geneticist Ami Bhatt was intrigued by widespread reports of vomiting and diarrhoea in people infected with SARS-CoV-2. “At that time, this was thought to be a respiratory virus,” she says. Bhatt and her colleagues, curious about a possible link between the virus and the gastrointestinal symptoms, began to collect stool samples from people with COVID-19. Thousands of miles away from Bhatt’s lab at Stanford Medicine in California, gastroenterology internist Timon Adolph was puzzled by accounts of gut symptoms in infected people. Adolph and his colleagues at the Medical University of Innsbruck in Austria started to assemble specimens, too — gastrointestinal-tissue biopsies. Two years into the pandemic, the scientists’ foresight has paid off: both teams have recently published results1,2 suggesting that pieces of SARS-CoV-2 can linger in the gut for months after an initial infection. The findings add to a growing pool of evidence supporting the hypothesis that persistent bits of virus — coronavirus “ghosts”, Bhatt has called them — could contribute to the mysterious condition called long COVID. Even so, Bhatt both urges scientists to keep an open mind and cautions that researchers have not yet nailed down a link between persistent viral fragments and long COVID. “Additional studies still need to be done — and they’re not easy,” she says.

Long COVID is often defined as symptoms that linger beyond 12 weeks after an acute infection. More than 200 symptoms have been associated with the disorder, which ranges in severity from mild to debilitating. Theories about its origins vary, and include harmful immune responses, tiny blood clots and lingering viral reservoirs in the body. Many researchers think that a mix of these factors contributes to the global burden of disease. An early hint that the coronavirus might persist in the body came in work3 published in 2021 by gastroenterologist Saurabh Mehandru at the Icahn School of Medicine at Mount Sinai in New York City and his colleagues. By then, it was clear that cells lining the gut display the protein that the virus uses to enter cells. This allows SARS-CoV-2 to infect the gut. Mehandru and his team found viral nucleic acids and proteins in gastrointestinal tissue collected from people who’d been diagnosed with COVID-19 an average of four months earlier. The researchers also studied participants’ memory B cells, which are pivotal players in the immune system. The team found that antibodies produced by these B cells were continuing to evolve, suggesting that, at six months after the initial infection, the cells were still responding to molecules made by SARS-CoV-2. Inspired by this work, Bhatt and her colleagues found that a few people continued to shed viral RNA into their stool seven months after an initial mild or moderate SARS-CoV-2 infection, well after their respiratory symptoms had ended.

Virus goes for the gut

Adolph says the 2021 paper inspired his team to look at their biopsy samples for signs of coronavirus. They found that 32 of 46 study participants who had had mild COVID-19 showed evidence of viral molecules in their gut seven months after acute infection. About two-thirds of those 32 people had long-COVID symptoms.

But all of the participants in this study had inflammatory bowel disease, an autoimmune disorder, and Adolph cautions that his data do not establish that there is active virus in these people, or that the viral material is causing long COVID. In the meantime, more studies have suggested lingering viral reservoirs beyond the gut. Another team of researchers has studied tissue collected from autopsies of 44 people who had been diagnosed with COVID-19 and found evidence of viral RNA in many sites, including the heart, eyes and brain4. Viral RNA and proteins were detected up to 230 days after infection. The study has not yet been peer reviewed.

Viral hideouts

Nearly all of the people in that sample had had severe COVID-19, but a separate study of two people who had had mild COVID-19 followed by long COVID symptoms found viral RNA in the appendix and the breast5. Pathologist Joe Yeong at the Institute of Molecular and Cell Biology at the Agency for Science, Technology, and Research in Singapore, who is a co-author of the report, which has not been peer reviewed, speculates that the virus might infiltrate and hide out in immune cells called macrophages, which can be found in a variety of the body’s tissues. All of these studies support the possibility that long-term viral reservoirs contribute to long COVID, but researchers will need to do more work to conclusively show a link, says Mehandru. They will need to document that the coronavirus is evolving in people who are not immunocompromised, and they will need to link such evolution to long COVID symptoms. “Right now there is anecdotal evidence, but there are a lot of unknowns,” Mehandru says Bhatt is hopeful that samples will become available to test the viral-reservoir hypothesis. The US National Institute of Health, for example, is running a large study called RECOVER, which aims to tackle the causes of long COVID and will collect biopsies from the lower intestines of some participants. But Sheng says he does not need to wait for a billion-dollar study to get more samples: an organization of people with long COVID has contacted him and offered to send samples from members who have had biopsies for various reasons, such as a cancer diagnosis, after their infections. “It’s really random, the tissue can come from everywhere,” he says. “But they don’t want to wait.”

Published in Nature (May 11, 2022):

https://doi.org/10.1038/d41586-022-01280-3