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New Coronavirus Variants Are Urgently Being Tracked around the World

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COVID appears to be in retreat in the U.S. and other nations that have widespread access to vaccines. But some developing countries with high infection rates have become hotspots for viral variants that may be more transmissible or resistant to vaccines–and these variants can quickly cross national borders. For example, the B.1.167.2 variant (now dubbed Delta) that was first detected in India has spread to more than 70 countries and regions, including the U.S.


Much of the developing world lacks the capacity for viral surveillance–efforts to monitor the spread and evolution of new variants. This process requires expensive genomic-sequencing technology and trained workforces that many nations do not have. Nepal, for instance, has sequenced just 0.01 percent of the more than 600,000 cases reported in the country so far. New variants could undo hard-won progress in curbing the pandemic, according to Alina Chan, a postdoctoral fellow specializing in gene therapy and cell engineering at the Broad Institute of the Massachusetts Institute of Technology and Harvard University. “Variants that evolve to be able to reinfect previously infected people are likely to also reduce the efficacy of vaccines,” she says.


Scientists and organizations around the world are now working to build capacity to hunt for variants in developing countries. They are mobilizing to deliver funds, training and equipment to where these resources are needed most, with aspirations of creating a lasting viral surveillance infrastructure. “COVID is the catalyst,” says Jairo Mendez-Rico, a microbiologist and adviser on viral diseases at the Pan American Health Organization (PAHO), headquartered in Washington, D.C. “But we also need to survey for other pathogens that for sure will come in the future.”


In India, 27 laboratories have now banded together to create the Indian SARS-CoV-2 Genomics Consortium (INSACOG). The group plans to sequence 5 percent of all positive COVID cases in the country (the current rate is only 0.09 percent). Shahid Jameel, a virologist and director of the Trivedi School of Biosciences at India’s Ashoka University, says that bringing existing surveillance capacity under a single umbrella could, in principle, make that a feasible goal. But there are not enough trained field-workers, he says, and the laboratories have acute shortages of chemical reagents needed for genomic analyses.


International experts are now stepping in to help. Recently, a nonprofit volunteer group called INDIA COVID SOS formed to assist with the pandemic response in the country. It aims to scale genomic surveillance across India, as well among neighboring South Asian nations. Aditi Hazra, an epidemiologist at Harvard Medical School, co-leads the group’s sequencing team, which meets regularly on video conference calls with the directors of India’s sequencing consortium. She says a key objective is to extend viral surveillance to more people in rural areas, where much of the population lives.


Rural surveillance is a priority in Africa as well. Millions of people on the continent live in remote areas that “are also hot spots for disease outbreaks,” says Akaninyene Otu, a medical doctor and a senior lecturer at the University of Calabar in Nigeria. Several new partnerships aim to boost sequencing in African countries. Otu highlights the Africa Pathogen Genomics Initiative (Africa PGI), which launched last year with support from international donor organizations and private companies. Most of the sequencing capacity in Africa is concentrated in South Africa, Kenya, Nigeria, Morocco and Egypt. The Africa PGI, which is headed by the Africa Centers for Disease Control and Prevention, is setting out to create a pan-African network of sequencing centers to serve the continent’s 54 countries.


In Latin American countries–which are currently reporting some of the highest COVID infection rates in the world–PAHO is spearheading the COVID-19 Genomic Surveillance Regional Network. Some countries in the region already have fairly strong sequencing capabilities, but the network is leading efforts to build surveillance capacity where it does not exist at all, which is the case throughout much of Central America. In the interim, two large reference labs–one in Brazil and one in Chile–are sequencing samples sent by other countries “at PAHO’s expense,” Mendez-Rico says.




In addition to building partnerships and networks, scientists are also exploring low-cost sequencing technologies that could be deployed easily in the field. Nearly all of the SARS-CoV-2 cases sequenced so far have relied on large, expensive instruments housed in climate-controlled lab facilities. As an alternative, INDIA COVID SOS is encouraging wider use of a handheld sequencing device made by Oxford Nanopore Technologies in England. The device, called the MinION, can run on a battery pack, processes 96 samples at a time and uses software to generate whole genome sequences that can be stored on a laptop. “We’re looking for technologies that are cheap, efficient, scalable and portable, and this is an example,” Hazra says.


Keith Robison, a computational biologist at Ginkgo Bioworks, a Boston-based biotechnology company, agrees that the MinION is a practical option for developing nations–especially in rural settings. The portable technology was widely used during the recent Ebola outbreaks in the Democratic Republic of the Congo and other West African countries. “You can generate sequences with it from anywhere,” he says. The MinION has its drawbacks: the quality of the data is not as good as what the lab-based instruments provide, Robison notes. “However, that can also be computationally corrected if you have many copies of the same sequence,” he says.


Tue Sparholt Jorgensen, a postdoctoral researcher in microbiology at the Technical University of Denmark, argues that whole-genome sequences may not always be needed. All the important SARS-CoV-2 mutations identified so far, he says, sit on the same stretch of genome encoding the microbe’s well-known spike protein. Jorgensen says scientists can simply target this piece of the viral geome with an alternative method called Sanger sequencing. This method, which was used as part of the effort that led to the sequencing of the complete human genome back in 2003, is still employed by labs all over the world. Unlike whole-genome methods that sequence millions of genetic fragments simultaneously, the Sanger method sequences one fragment at a time. “Sanger can’t replace whole-genome sequencing, but you can use it for targeted analyses at a fraction of the cost,” Jorgensen says. “People have been using it in small labs for decades. I’d use it to monitor for known variants, [to] qualify samples for whole genome sequencing and for contact tracing [of infected people] in hospitals.”


Jorgensen and his colleagues are now working with health officials in Rwanda on plans to expand Sanger-based COVID surveillance in the country. “If a new variant emerges in Rwanda and starts spreading [elsewhere] in Africa, then we want to know about it,” he says.

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COVID, Quickly, Episode 9: Delta Variant, Global Vaccine Shortfalls, Beers for Shots

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Today we bring you a new episode in our podcast series: COVID, Quickly. Every two weeks, Scientific American‘s senior health editors Tanya Lewis and Josh Fischman catch you up on the essential developments in the pandemic: from vaccines to new variants and everything in between.

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Coronavirus News Roundup: June 5 to June 18

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The items below are highlights from the free newsletter, “Smart, useful, science stuff about COVID-19.” To receive newsletter issues daily in your inbox, sign up here.


Novavax reports that its two-dose protein-based vaccine against COVID-19 has been 100% effective in preventing severe illness, hospitalization and death due to COVID-19, as well as 90.4% effective against COVID-19 symptoms in large-scale human studies. These studies, which involved thousands of people in the U.S. and Mexico, showed that the vaccine also was highly effective against “Alpha,” the SARS-CoV-2 variant first identified in Great Britain, reports Carl Zimmer at The New York Times (6/14/21). “Novavax plans to apply for authorization in UK, EU, India, South Korea, and possibly the U.S.,” according to an Unbiased SciPod post (6/15/21).


A 6/17/21 story by Tanya Lewis at Scientific American describes some of the incentives being offered to people for getting vaccinated against COVID-19 — including lottery tickets, college scholarships, train tickets, firearms, cash pay-outs, cannabis joints, doughnuts, free trips, cruises, and gift certificates. “Public health experts use incentives all the time to get people to quit smoking, exercise more, and so on,” the story describes the director of the Health Decision Sciences Center at Massachusetts General Hospital’s general medicine division as saying. An unpublished study by the Mass General researcher suggests that incentives might effectively induce people to get a COVID-19 vaccine, Lewis reports. But for some people the best inducement is an opportunity to stop wearing a mask and a general return to normalcy, the story suggests.


Some positive news for people who have transplanted organs and thus take immune-suppressing drugs: a third dose of a mRNA vaccine against COVID-19 provoked a stronger immune response, at least in the form of antibodies, in organ transplant patients than the standard two doses did, per various reports. The findings, from a small study of patients who received a third dose this spring, were published 6/15/21 in Annals of Internal Medicine. The findings are “part of a broader discussion about whether and when to offer extra doses to vulnerable individuals,” writes Jennifer Couzin-Frankel at Science (6/14/21). In past studies, organ transplant patients who got a two-dose COVID-19 vaccine were far less likely to make protective antibodies against SARS-CoV-2 than the general population was. Some larger three-dose studies among people with compromised immune systems are under way, Couzin-Frankel reports. A medical oncologist at the University of Pennsylvania is not very worried about the effectiveness of COVID-19 vaccines among people with cancer, the story states. The story then describes two recent studies of cancer patients showing that they produced antibodies against SARS-CoV-2 after receiving a COVID-19 vaccine. However, a third study found much lower antibody levels among vaccinated cancer patients than it did among their healthy family members who also were vaccinated, Couzin-Frankel reports.


The Unbiased SciPod posted some helpful informational graphics about Pfizer’s ongoing studies of its COVID-19 vaccine in children under 12 (6/11/21). The post states that dosages have been set based on initial smaller studies in children (one-third the adult dose for ages 5-11 and one-tenth the adult dose for ages 6 months to 5 years), and that researchers will enroll 4,500 children across 90 sites globally for the larger safety and effectiveness studies. “Children have immune system components that are more potent compared to adults. They may not need as high a dose for protection. Age criteria are related to immune system development, not physical size,” the post states. The results will likely become available this fall for review by the U.S. Food and Drug Administration, with a first batch — from studies in children ages 5 to 11 — expected in early September, the post states.


Nearly one quarter of all people in the U.S. who were infected with SARS-CoV-2 last year, including 19% of those who never reported COVID-19 symptoms from their infection, had new medical problems within a month or more of recovering from the virus, according to a large study covered by Pam Belluck at The New York Times (6/15/21). Belluck writes: “Those affected were all ages, including children. Their most common new health problems were pain, including in nerves and muscles; breathing difficulties; high cholesterol; malaise and fatigue; and high blood pressure. Other issues included intestinal symptoms; migraines; skin problems; heart abnormalities; sleep disorders; and mental health conditions like anxiety and depression.” The study, conducted by non-profit organization FAIR Health and not formally reviewed by experts for flaws, involved evaluating electronic health-insurance records.


A 6/11/21 story by Emily Anthes at The New York Times runs down some evidence-based approaches that employers can take to reduce the risk of SARS-Cov-2 infections and other health problems as workers return to offices nationwide. Employers should flush unused taps and other plumbing to clear any metals or Legionella bacteria colonies that accumulated, the story states. Employers also should upgrade their ventilation and filtration systems, the story states. The goal is four to six air changes per hour, the story states, which is equivalent to completely refreshing air every 10 to 15 minutes in a room. Portable air purifiers or even “desktop level HEPA filters” can help. And continue to wash your hands routinely, for at least 20 seconds each time, advises a Northwestern University environmental microbiologist who is quoted in the story. Not solutions: desk shields (plexiglass barriers are a good idea in grocery stores though), foggers, fumigators, ionizers, ozone generators and other ‘air cleaning’ devices,’ the story states. In most non-medical or non-lab settings, wiping down surfaces with bleach solutions or disinfectant solutions or wipes does little to prevent SARS-CoV-2 transmission. Besides, inhaling these substances is harmful. “The no. 1 thing is to get vaccinated,” the story quotes Joseph Allen at the Harvard School of Public Health as saying.


A debate among scientists about whether SARS-CoV-2 spreads mainly by fallen respiratory droplets on surfaces that people touch or spreads in air hampered public health efforts to control the pandemic and to prevent deaths. The implications for this debate were crucial, as Megan Molteni at Wired writes (5/13/21) — officials need to know whether public-health messages should focus on hand washing or on masking and isolation or both, particularly before vaccines become available. The general debate is over, as you probably know — the virus is mostly spread in indoor air. But why did researchers disagree until recently? In part, it’s because the arguments against airborne SARS-CoV-2 all rested on an assumption that only particles smaller than 5 microns could hang in the air; larger ones, aka droplets, fall to surfaces. But in reality, larger particles can stay afloat and behave like aerosols, many scientists and engineers have known, including aerosols expert Linsey Marr of Virginia Tech, Molteni and others have written. Molteni’s story masterfully traces the events, conversations, and research that came to expose the “fallacy of the 5-micron boundary.” The hero of this engaging story is Katie Randall, a graduate student who specializes in detective work to figure out how bits of knowledge are passed along through published research papers over time.


Guidance from the U.S. Centers for Disease Control in April stated that international and domestic travel are low-risk activities for people vaccinated against COVID-19 (so, this does not pertain, unfortunately, to U.S. children under 12, for whom COVID-19 vaccines are not yet authorized). In response to that update, Ceylan Yeginsu at The New York Times has written up answers to some of the questions that vaccinated travelers have these days (6/15/21). A summary of the answers (again, this information is all for vaccinated people in the U.S.): 1) Yes, you must still wear a mask at the airport and on flights; 2) No, you don’t have to quarantine or test if you travel domestically, unless it is required by a state or territory; 3) No, you don’t have to take a coronavirus test before departure to international destinations — not for the U.S. at least; check for your destination; 4) Yes, you have to test, even if vaccinated, three days before you return by air to the U.S.; 5) Check lists of countries that will accept people from the U.S. under certain conditions, including some destinations in Europe and the Caribbean.


Scientists at the Walter Reed Army Institute of Research in Maryland are working on a vaccine that could protect us against all coronaviruses. In this 6/9/21 podcast at Scientific American, Emily Mullins interviews Dr. Kayvon Modjarrad who is leading the effort at Walter Reed to develop a so-called universal coronavirus vaccine. The vaccine candidate that is being tested “combines nanoparticles from a blood protein called ferritin with coronavirus proteins.” (Sorry, I’m not sure what that means either.) Modjarrad says 200 different combinations of spike proteins (a type of complex molecules that are found on the surface of all coronaviruses), types of ferritin, and ways to link them eventually yielded a vaccine candidate that repeatedly provoked a strong immune response against SARS-CoV-1, SARS-CoV-2 and three of its variants in several species of animals ranging from rodents to sharks. The vaccine now is being tested in a small group of humans. “If it works and is safe, it could provide a foundation for a universal coronavirus vaccine,” Mullin says.


You might enjoy, “A lexicon for the late pandemic,” by Jay Martel for The New Yorker (6/14/21).

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How End-of-Life Doulas Help Ease the Final Transition

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Birth and death are the bookends of life, yet we welcome one and dread the other. Why is it that birth is celebrated, but death is taboo?


When a friend was expecting her first child, she needed additional support through her pregnancy, so she hired a birth doula. The idea of women helping other women during childbirth is not new. Since the beginning of time, women have labored and birthed at home, attended by a midwife and their female friends and kin. This camaraderie of women, once universal, was a way to provide birth support and also to pass on knowledge about pregnancy, childbirth and parenting.


The natural birth movement of the 1960s begged a return to this approach with women demanding unmedicated, less interventional births. Hence, the inception of the birth doula–a nonmedical caregiver who assisted pregnant women in the transition to motherhood.


Can the same idea apply to death? The evolution of death care has followed a similar trajectory to that of childbirth care. For most of human history, people were cared for and died at home, with corpses even displayed on the dining room table for mourning. This began to change in the mid-20th century as society saw great advancements in medical technology for diagnosis and treatment of illnesses. These developments moved health care away from the local doctor, who made house calls, to inpatient stays at hospitals. When people fell ill, they went to the hospital and eventually died there. In 1980, 60.5 percent of people died in hospitals. This number peaked in the mid-1980’s, but has since steadily decreased in response to a growing movement for death to be less medicalized, less institutionalized, and more natural. By 2016, half as many people (29.4 percent) were dying in hospitals, roughly equaling the number of people dying at home (30.5 percent). While this trend is encouraging, these numbers still do not reflect the fact that 71 percent of people would prefer to die at home.


I am a death doula, or what is now more commonly termed an end-of-life doula. This role grew out of the increasing awareness of and desire for more humane and compassionate ways to die. Similar to birth doulas, end-of-life doulas are nonmedical professionals offering emotional, spiritual, informational and physical support–not at birth, but at the other end of the spectrum of life–at death.


An elderly man with a terminal illness is afraid to die. He fears for the family he will leave behind–his wife, children and grandchildren–and how they will cope after he is gone. He has not expressed this fear to his doctors or to his wife, who is already handling so much. I listen. I hold space for his despair and angst. He realizes the fear is based on his immense love for his family. He drinks champagne with them on his deathbed. Reconciliation with the things that are important can allow one the peace to let go.


End-of-life doulas work with those with serious illnesses who are facing death–and also for those who are healthy and just want to prepare for death. On practical matters, doulas can advise on advance care directives, vigil planning and postdeath options, and assist with life review and legacy. On more emotional matters, doulas can facilitate conversations about unresolved issues or complex family dynamics and offer space for the fears and uncertainties around death and dying. When we are prepared for death, we are better able to face it when the time comes.


Despite her wish to die at home, an elderly woman is taken to the hospital by her son, who can no longer bear to watch his mother die in excruciating pain. The hospital wants to discharge her, finding nothing wrong, and, at her age, what can be done anyhow? The family is distressed by the hospital’s response and calls me. I suggest that they ask for a palliative care consultation. Eventually, the mother is placed on a proper pain management plan and discharged to hospice care. How do you know what to ask for, if you don’t know the choices?


Palliative and hospice care are philosophies of care that focus on comfort and symptom management to alleviate pain and suffering. Both are available to persons with serious illnesses. While palliative care can be given concurrently with curative care, hospice is typically for those who no longer seek curative treatments.


End-of-life doulas advocate for the wishes and needs of the dying person. We work with the health care team in ongoing care and coordinate with the support network of family and friends in place or help to establish a needed support system. We fill gaps in care and tackle tasks that are difficult to do or face. All the while, we can be a calming presence for loved ones and the dying person, especially for those who are facing death all alone.


A middle-aged man lies actively dying, completely nonresponsive, in his bed. He displays “death rattle” breathing, and his body has occasional violent spasms. At his bedside, a petite woman sits, his aunt, pained to watch her nephew die this way. After creating rapport with the aunt, I seek to allay her distress and encourage her to speak to him. The aunt responds gratefully, awakened to the possibility of making a difference for her nephew. He dies peacefully, immersed in soft light, music and love. Sometimes all a loved one needs is permission to be an active participant in the process, to turn helplessness into empowerment.


While death brings sadness and loss, there can also be positive emotions of love, honor and pride. It is possible to feel seemingly contradictory emotions all at the same time–because death is loss, and grief is the natural expression of love.


On the end-of-life journey, we doulas are your personal advocate, cheerleader, companion, guide, ear, rock–whatever you need us to be to face a difficult, intense and emotional time, because no one who wants support at the end of life should have to go without.


This is an opinion and analysis article.

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