Genes shape our response to Covid virus
Important findings are starting to emerge from research on how genes shape the human response to the Covid virus.
From infections with no symptoms to why men are more likely to be hospitalized in the ICU and die of COVID-19, new research shows that your genes play a significant role
Early in the pandemic, genetic research focused on the virus because it was readily available. Plus, the virus contains only 30,000 bases in a dozen functional genes, so it's relatively easy and affordable to sequence. Additionally, the rapid mutation of the virus and its ability to escape antibody control fueled waves of different variants and provided a reason to follow viral genetics.
In comparison, there are many more genes of the human immune system and cellular functions that affect viral replication, with about 3.2 billion base pairs. Human studies require samples from large numbers of people, the analysis of each sample is vastly more complex, and sophisticated computer analysis often is required to make sense of the raw data. All of this takes time and large amounts of money, but important findings are beginning to emerge.
Asymptomatics
About half the people exposed to SARS-CoV-2, the virus that causes the COVID-19 disease, never develop symptoms of this disease, or their symptoms are so mild they often go unnoticed. One piece of understanding the phenomena came when researchers showed that exposure to OC43, a common coronavirus that results in symptoms of a cold, generates immune system T cells that also help protect against SARS-CoV-2.
Jill Hollenbach, an immunologist at the University of California at San Francisco, sought to identify the gene behind that immune protection. Most COVID-19 genetic studies are done with the most seriously ill patients because they are hospitalized and thus available. “But 99 percent of people who get it will never see the inside of a hospital for COVID-19,” she says. “They are home, they are not interacting with the health care system.”
Early in the pandemic, when most labs were shut down, she tapped into the National Bone Marrow Donor Program database. It contains detailed information on donor human leukocyte antigens (HLAs), key genes in the immune system that must match up between donor and recipient for successful transplants of marrow or organs. Each HLA can contain alleles, slight molecular differences in the DNA of the HLA, which can affect its function. Potential HLA combinations can number in the tens of thousands across the world, says Hollenbach, but each person has a smaller number of those possible variants.
She teamed up with the COVID-19 Citizen Science Study a smartphone-based study to track COVID-19 symptoms and outcomes, to ask persons in the bone marrow donor registry about COVID-19. The study enlisted more than 30,000 volunteers. Those volunteers already had their HLAs annotated by the registry, and 1,428 tested positive for the virus.
Analyzing five key HLAs, she found an allele in the gene HLA-B*15:01 that was significantly overrepresented in people who didn’t have any symptoms. The effect was even stronger if a person had inherited the allele from both parents; these persons were “more than eight times more likely to remain asymptomatic than persons who did not carry the genetic variant,” she says. Altogether this HLA was present in about 10 percent of the general European population but double that percentage in the asymptomatic group. Hollenbach and her colleagues were able confirm this in other different groups of patients.
What made the allele so potent against SARS-CoV-2? Part of the answer came from x-ray crystallography. A key element was the molecular shape of parts of the cold virus OC43 and SARS-CoV-2. They were virtually identical, and the allele could bind very tightly to them, present their molecular antigens to T cells, and generate an extremely potent T cell response to the viruses. And “for whatever reasons that generated a lot of memory T cells that are going to stick around for a long time,” says Hollenbach. “This T cell response is very early in infection and ramps up very quickly, even before the antibody response.”
Understanding the genetics of the immune response to SARS-CoV-2 is important because it provides clues into the conditions of T cells and antigens that support a response without any symptoms, she says. “It gives us an opportunity to think about whether this might be a vaccine design strategy.”
Dead men
A researcher at the Leibniz Institute of Virology in Hamburg Germany, Guelsah Gabriel, was drawn to a question at the other end of the COVID-19 spectrum: why men more likely to be hospitalized and die from the infection. It wasn't that men were any more likely to be exposed to the virus but more likely, how their immune system reacted to it
Several studies had noted that testosterone levels were significantly lower in men hospitalized with COVID-19. And, in general, the lower the testosterone, the worse the prognosis. A year after recovery, about 30 percent of men still had lower than normal levels of testosterone, a condition known as hypogonadism. Most of the men also had elevated levels of estradiol, a female hormone (https://pubmed.ncbi.nlm.nih.gov/34402750/).
Every cell has a sex, expressing receptors for male and female hormones on their surface. Hormones docking with these receptors affect the cells' internal function and the signals they send to other cells. The number and role of these receptors varies from tissue to tissue.
Gabriel began her search by examining whole exome sequences, the protein-coding part of the genome, for key enzymes involved in the metabolism of sex hormones. The research team quickly zeroed in on CYP19A1, an enzyme that converts testosterone to estradiol. The gene that produces this enzyme has a number of different alleles, the molecular variants that affect the enzyme's rate of metabolizing the sex hormones. One genetic variant, CYP19A1 (Thr201Met), is typically found in 6.2 percent of all people, both men and women, but remarkably, they found it in 68.7 percent of men who were hospitalized with COVID-19.
Lung surprise
Lungs are the tissue most affected in COVID-19 disease. Gabriel wondered if the virus might be affecting expression of their target gene in the lung so that it produces more of the enzyme that converts testosterone to estradiol. Studying cells in a petri dish, they saw no change in gene expression when they infected cells of lung tissue with influenza and the original SARS-CoV viruses that caused the SARS outbreak in 2002. But exposure to SARS-CoV-2, the virus responsible for COVID-19, increased gene expression up to 40-fold, Gabriel says.
Did the same thing happen in humans? Autopsy examination of patients in three different cites found that “CYP19A1 was abundantly expressed in the lungs of COVID-19 males but not those who died of other respiratory infections,” says Gabriel. This increased enzyme production led likely to higher levels of estradiol in the lungs of men, which “is highly inflammatory, damages the tissue, and can result in fibrosis or scarring that inhibits lung function and repair long after the virus itself has disappeared.” Somehow the virus had acquired the capacity to upregulate expression of CYP19A1.
Only two COVID-19 positive females showed increased expression of this gene. The menopause status of these women, or whether they were on hormone replacement therapy was not known. That could be important because female hormones have a protective effect for cardiovascular disease, which women often lose after going through menopause, especially if they don’t start hormone replacement therapy. That sex-specific protection might also extend to COVID-19 and merits further study.
The team was able to confirm their findings in golden hamsters, the animal model of choice for studying COVID-19. Testosterone levels in male animals dropped 5-fold three days after infection and began to recover as viral levels declined. CYP19A1 transcription increased up to 15-fold in the lungs of the male but not the females. The study authors wrote, “Virus replication in the male lungs was negatively associated with testosterone levels.”
The medical community studying COVID-19 has slowly come to recognize the importance of adipose tissue, or fat cells. They are known to express abundant levels of CYP19A1 and play a significant role as metabolic tissue in COVID-19. Gabriel adds, “One of the key findings of our study is that upon SARS-CoV-2 infection, the lung suddenly turns into a metabolic organ by highly expressing” CYP19A1.
She also found evidence that SARS-CoV-2 can infect the gonads of hamsters, thereby likely depressing circulating levels of sex hormones. The researchers did not have autopsy samples to confirm this in humans, but others have shown that the virus can replicate in those tissues.
A possible treatment
Back in the lab, substituting low and high doses of testosterone in SARS-COV-2 infected male hamsters had opposite effects depending on testosterone dosage used. Gabriel says that hormone levels can vary so much, depending on health status and age and even may change throughout the day, that “it probably is much better to inhibit the enzyme” produced by CYP19A1 than try to balance the hormones.
Results were better with letrozole, a drug approved to treat hypogonadism in males, which reduces estradiol levels. The drug also showed benefit in male hamsters in terms of less severe disease and faster recovery. She says more details need to be worked out in using letrozole to treat COVID-19, but they are talking with hospitals about clinical trials of the drug.
Gabriel has proposed a four hit explanation of how COVID-19 can be so deadly for men: the metabolic quartet. First is the genetic risk factor of CYP19A1 (Thr201Met), then comes SARS-CoV-2 infection that induces even greater expression of this gene and the deleterious increase of estradiol in the lung. Age-related hypogonadism and the heightened inflammation of obesity, known to affect CYP19A1 activity, are contributing factors in this deadly perfect storm of events.
Studying host genetics, says Gabriel, can reveal new mechanisms that yield promising avenues for further study. It’s also uniting different fields of science into a new, collaborative approach they’re calling “infection endocrinology,” she says.
Should egg and sperm donors reveal their identities? The debate pivots on genetics and medical history.
Cassandra Adams performs on stage at the Jersey City Theater Center in March 2019 to raise awareness about traumatic experiences that she and others have had with anonymous donor conception.
Until age 35, Cassandra Adams assumed her mother and father were her biological parents. Then she took saliva tests through two genealogy databases—23andMe and AncestryDNA—and discovered a discrepancy in her heritage. In bringing up the matter with her parents, she learned that fertility issues had led the couple to use a sperm donor.
“Most people my age were not told,” said Adams, now 40 and a stay-at-home mom in Jersey City, New Jersey, who is involved with donor-conception advocacy. “Even now, there’s still a lot of secrecy in the industry. There are still many parents who aren’t truthful or planning not to be truthful with their children.”
While some of those offspring may never know a significant part of their medical history, Adams is grateful that she does. Surprisingly, the DNA test revealed Jewish ancestry.
“There are a lot more genetic conditions that run in Jewish families, so it was really important that I get my medical history, because it’s very different from my dad who raised me,” said Adams, who has met her biological father and two of three known half-siblings. As a result of this experience, she converted to Judaism. “It has been a big journey,” she said.
In an era of advancing assisted reproduction technologies, genetics and medical history have become front and center of the debate as to whether or not egg and sperm donations should be anonymous – and whether secrecy is even possible in many cases.
Obstacles to staying anonymous
People looking to become parents can choose what’s called an “identity-release donor,” meaning their child can receive information about the donor when he or she turns 18. There’s no way to ensure that the donor will consent to a relationship at that time. Instead, if a relationship between the donor and child is a priority, parents may decide to use a known donor.
The majority of donors want to remain anonymous, said reproductive endocrinologist Robert Kiltz, founder and director of CNY Fertility in Syracuse, New York. “In general, egg and sperm donation is mostly anonymous, meaning the recipient doesn’t know the donor and the donor doesn’t know the recipient.”
Even if the donor isn’t disclosed, though, the mystery may become unraveled when a donor-conceived person undergoes direct-to-consumer genetic testing through ancestry databases, which are growing in number and popularity. These services offer DNA testing and links to relatives with identifiable information.
In the future, another obstacle to anonymity could be laws that prohibit anonymous sperm and egg donations, if they catch on. In June, Colorado became the first state in the nation to ban anonymous sperm and egg donations. The law, which takes effect in 2025, will give donor-conceived adults the legal authority to obtain their donor’s identity and medical history. It also requires banks that provide sperm and egg collection to keep current medical records and contact information for all donors. Meanwhile, it prohibits donations from those who won’t consent to identity disclosures.
“The tradition of anonymous sperm or egg donation has created a vast array of problems, most significantly that the people thus created want to know who their mommy and daddy are,” said Kenneth W. Goodman, professor and director of the Institute for Bioethics and Health Policy at the University of Miami Miller School of Medicine.
“There are counter arguments on both sides. But the current situation has led to great uncertainty and, in many cases, grief,” Goodman said.
Donors should bear some moral responsibility for their role in reproduction by allowing their identity to be disclosed to donor-conceived individuals when they turn 18, Goodman added, noting that “there are counter arguments on both sides. But the current situation has led to great uncertainty and, in many cases, grief.”
Adams, the Jersey City woman who learned she was Jewish, has channeled these feelings into several works of art and performances on stage at venues such as the Jersey City Theater Center. During these performances, she describes the trauma of “not knowing where we come from [or] who we look like.”
In the last five years, Kathleen “Casey” DiPaola, a lawyer in Albany, New York, who focuses her practice on adoption, assisted reproduction and surrogacy, has observed a big shift toward would-be parents looking to use known sperm donors. On the other hand, with egg donation, “I’m not seeing a whole lot of change,” she said. Compared to sperm donation, more medical screening is involved with egg donation, so donors are primarily found through fertility clinics and egg donor agencies that prefer anonymity. This leads to fewer options for prospective parents seeking an egg donor with disclosed identity, DiPaola said.
Some donors want to keep in touch
Rachel Lemmons, 32, who lives in Denver, grew interested in becoming an egg donor when, as a graduate student in environmental sciences, she saw an online advertisement. “It seemed like a good way to help pay off my student loan debt,” said Lemmons, who is married and has a daughter who will turn 2-years-old in December. She didn’t end up donating until many years later, after she’d paid off the debt. “The primary motivation at that point wasn’t financial,” she said. “Instead, it felt like a really wonderful way to help someone else have a family in a few weeks’ time.”
Lemmons originally donated anonymously because she didn’t know open donations existed. She was content with that until she became aware of donor-conceived individuals’ struggles. “It concerned me that I could potentially be contributing to this,” she said, adding that the egg donor and surrogacy agency and fertility clinic wouldn’t allow her to disclose her identity retroactively.
Since then, she has donated as an open donor, and kept in touch with the recipients through email and video calls. Knowing that they were finally able to have children is “incredibly rewarding,” Lemmons said.
When to tell the kids
Stanton Honig, professor of urology and division chief of sexual and reproductive medicine at Yale School of Medicine, said for years his team has recommended that couples using donor sperm inform children about the role of the donor and their identity. “Honesty is always the best policy, and it is likely that when they become of age, they might or will be able to find out about their biological sperm donor,” he said. “Hiding it creates more of a complicated situation for children in the long run.”
Amy Jones, a 45-year-old resident of Syracuse, N.Y., has three children, including twins, who know they were conceived with anonymous donor eggs from the same individual, so they share the same genetics. Jones, who is a registered nurse and asked for her real name not to be published, told them around age seven.
“The thought of using a known donor brought more concerns—what if she wanted my babies after they were born, or how would I feel if she treated them as her own every time I saw her?” said Jones.
“I did a lot of reading, and all psychologists said that it is best to start the conversation early,” she recalled. “They understood very little of what I was telling them, but through the years, I have brought it up in discussion and encouraged them to ask questions. To this day, they don't seem to be all that interested, but I expect that later on in life they may have more questions.”
Jones and her husband opted to use a donor because premature ovarian failure at age 27 had rendered her infertile. “The decision to use an egg donor was hard enough,” she said. “The thought of using a known donor brought more concerns—what if she wanted my babies after they were born, or how would I feel if she treated them as her own every time I saw her?”
Susan C. Klock, a clinical psychologist in the section of fertility and reproductive medicine at Northwestern University Feinberg School of Medicine, said, “Anonymity is virtually impossible in the age of direct-to-consumer genetic testing.” In addition, “selecting an identity-release donor is typically not the first thing parents are looking at when they select a donor. First and foremost, they are looking for a donor with a healthy medical background. Then they may consider donor characteristics that resemble the parents.”
The donor’s medical history can be critical
Donor agencies rely on the self-reported medical history of egg and sperm donors, which can lead to gaps in learning important information. Knowing a donor’s medical history may have led some families to make different or more well-informed choices.
After Steven Gunner, a donor-conceived adult, suffered from schizophrenia and died of a drug overdose at age 27 in 2020, his parents, who live in New York, learned of a potential genetic link to his mental illness. A website, Donor Sibling Registry, revealed that the sperm donor the couple had used, a college student at the time of donation, had been hospitalized during childhood for schizophrenia and died of a drug overdose at age 46. Gunner’s story inspired Steven’s Law, a bill that was introduced in Congress in July. If passed, it would mandate sperm banks to collect information on donors’ medical conditions, and donors would have to disclose medical information the banks weren’t able to find.
With limited exceptions, the U.S. Food and Drug Administration requires donors to be screened and tested for relevant communicable disease agents and diseases such as HIV, hepatitis viruses B and C, the Zika virus and several STDs. With current technology, it is also impossible to screen for thousands of rare genetic diseases. “If a couple is using IVF (in vitro fertilization) to conceive with the donor gamete, some may opt for pre-implantation genetic testing to assess for chromosomal abnormalities,” Klock said.
Even these precautions wouldn't cover every disease, and some would-be parents don't get the genetic screening. In a situation where one donor has a large number of offspring, it is concerning that he or she can spread a rare disease to multiple people, said Nick Isel, 37, of Yorkville, Illinois, who was conceived with donor sperm due to his parents’ fertility issues. They told him the truth when he was a teenager, and he found his biological father with a journalist’s help.
Since 2016, Isel, who owns a roofing company, has been petitioning the FDA to extend the retention of medical records, requiring the fertility establishment to maintain information on sperm and egg donors for 50 years instead of the current 10-year mandate.
“The lack of family health information,” he said, “is an ongoing, slow-motion public health crisis since donor conception began being regulated by the FDA as a practice.”
Saliva May Help Diagnose PTSD in Veterans
A recent study finds that former soldiers with post traumatic stress disorders have a certain set of bacteria in their saliva, a distinct signature that is believed to be the first biological marker for PTSD.
As a bioinformatician and young veteran, Guy Shapira welcomed the opportunity to help with conducting a study to determine if saliva can reveal if war veterans have post-traumatic stress disorder, or PTSD.
The research team, which drew mostly from Tel Aviv University’s Sackler Faculty of Medicine and Sagol School of Neuroscience, collected saliva samples from approximately 200 veterans who suffered psychological trauma stemming from the years they spent fighting in the First Lebanon War in 1982. The researchers also characterized the participants’ psychological, social and medical conditions, including a detailed analysis of their microbiomes.
They found that the former soldiers with PTSD have a certain set of bacteria in their saliva, a distinct microbiotic signature that is believed to be the first biological marker for PTSD. The finding suggests that, in the future, saliva tests could be used to help identify this disorder. As of now, PTSD is often challenging to diagnose.
Shapira, a Ph.D. student at Tel Aviv University, was responsible for examining genetic and health-related data of the veterans who participated – information that had been compiled steadily over four decades. The veterans provided this data voluntarily, Shapira says, at least partly because the study carries important implications for their own psychological health.
The research was led by Illana Gozes, professor emerita of clinical biochemistry. “We looked at the bacteria in their blood and their saliva,” Gozes explains. To discover the microbial signatures, they analyzed the biometric data for each soldier individually and as a group. Comparing the results of the participants’ microbial distribution to the results of their psychological examinations and their responses to personal welfare questionnaires, the researchers learned that veterans with PTSD – and, more generally, those with significant mental health issues – have the same bacterial content in their saliva.
“Having empirical metrics to assess whether or not someone has PTSD can help veterans who make their case to the Army to get reparations,” Shapira says.
More research is required to support this finding, published in July in Nature’s prestigious Molecular Psychiatry, but it could have important implications for identifying people with PTSD. Currently, it can be diagnosed only through psychological and behavioral symptoms such as flashbacks, nightmares, sleep disorders, increased irritability and physical aggressiveness. Veterans sometimes don’t report these symptoms to health providers or realize they’re related to the trauma they experienced during combat.
The researchers also identified a correlation that indicates people with a higher level of education show a lower occurrence of the microbiotic signature linked to PTSD, while people who experienced greater exposure to air pollution show a higher occurrence of this signature. That confirms their finding that the veterans’ health is dependent on their individual biology combined with the conditions of their environment.
“Thanks to this study, it may be possible in the future to use objective molecular and biological characteristics to distinguish PTSD sufferers, taking into account environmental influences,” Gozes said in an article in Israel21c. “We hope that this new discovery and the microbial signatures described in this study might promote easier diagnosis of post-traumatic stress in soldiers so they can receive appropriate treatment.”
Gozes added that roughly a third of the subjects in their study hadn’t been diagnosed with PTSD previously. That meant they had never received any support from Israel’s Ministry of Defense or other officials for treatment and reparations, the payments to compensate for injuries sustained during war.
Shapira’s motivation to participate in this study is personal as well as professional: in addition to being veteran himself, his father served in the First Lebanon War. “Fortunately, he did not develop any PTSD, despite being shot in the foot...some of his friends died, so it wasn’t easy on him,” says Shapira.
“Having empirical metrics to assess whether or not someone has PTSD can help veterans who make their case to the Army to get reparations,” Shapira says. “It is a very difficult and demanding process, so the more empirical metrics we have to assess PTSD, the less people will have to suffer in these committees and unending examinations that are mostly pitched against the veterans because the state is trying to avoid spending too much money.”