U.S. races to catch up with other countries in COVID-19 sequencing research

 Medical experts have warned for months that the U.S. is falling far behind other countries in research on the evolution of the coronavirus, in both speed and comprehensiveness of approach. In early December, the discovery of a faster-spreading variant of COVID-19 in the U.K. lent urgency to the need for genetic sequencing that will help determine whether treatment regimens and vaccines remain effective against new mutations of the virus.

In the U.S., the first case of the U.K. variant B.1.17 was discovered in Colorado in December, and since then, at least 15 states have identified cases of the strain. Public health experts say it was already likely spreading here unseen, a casualty of the country's delayed COVID-19 sequencing campaign, and warned that other new homegrown variants could also be mutating without anyone's knowledge.

The U.S. is estimated to lag behind more than 30 nations in its sequencing effort, according to an analysis by the Broad Institute, from the global GISAID Initiative database.

But Colorado, where the first case of the faster-spreading U.K. variant was found in the U.S., is rushing to reverse this trend. The state has expanded its public health staff and equipment to speed its efforts. Its labs have identified the genetic sequencing of 1,400 samples so far and aim to sequence some 200 samples a week. 

The process of sequencing involves extracting and analyzing the unique genetic information in a virus sample to look for mutations. These findings help public health researchers track the spread of particular variants of the disease. While mutations are common and often harmless, the B.1.17 variant appears to spread more easily than previous strains. Both Pfizer and Moderna have said they believe their vaccines will still be effective against it.

Even before the Colorado case was identified, the state's health department laboratories were running diagnostic tests that could immediately flag potential samples with one of the U.K. variant's characteristic mutations. It was also training staff on new procedures to speed the search for the fast-moving bug.

Emily Travanty, scientific director with the Colorado Department of Public Health and Environment, said it "was truly a bit of luck" that the sample of the first U.K. case in the U.S. came into her lab.

"We don't have all of the samples in the whole state of Colorado, so that the sample came here to us and that we were on the lookout for it was sort of a bit of luck," Travanty said.

Some states have struggled to follow suit. The surge in coronavirus cases has forced labs to choose between diagnostic testing of the local population and sequencing the virus, a resource-intensive process that can last for days.

"More than anything else, the sequencing has come down to staffing," said Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories (APHL). She said APHL has heard from labs frustrated with "incredibly tight" supplies used both for sequencing and other laboratory work.

Researchers at the University of California Los Angeles were among those to abandon their sequencing work last year, amid a COVID spike in Southern California.

"We just didn't have the capacity," Omai Garner, director of clinical microbiology in the UCLA Health System, told CBS News.

"The people I would use for that sequencing are the same that were doing the diagnostic testing," added Garner.

As the Trump administration comes to an end, senior Biden transition officials say stepping up sequencing work will be a key priority in the funds requested from Congress as part of the president-elect's COVID-19 rescue proposal.

In November, the Centers for Disease Control and Prevention announced it was expanding its own capacity to collect and sequence coronavirus samples from health authorities around the country. Samples sent to CDC labs identified the first cases of B.1.1.7 in several states, including Texas, Indiana, and Pennsylvania, state public health officials tell CBS News.

This month, Illumina and LabCorp both announced new CDC contracts to sequence samples of SARS-CoV-2, the virus that causes COVID-19. Illumina has since identified 51 of the first 54 cases of the B.1.1.7 variant in the country.

The CDC also announced in December it was releasing some $15 million in funding to support local sequencing efforts through the Epidemiology and Laboratory Capacity (ELC) program, which has trickled out to some public health labs on the front lines of the pandemic.

A spokesperson for the Massachusetts State Public Health Laboratory said the agency had received $3.4 million in ELC funds, which had gone to new staff, equipment, and supplies. In Utah, officials said CARES Act funding and an ELC grant of some $176,000 had helped the state boost sequencing capacity to some 3,000 samples a day. And in Arkansas, a spokesperson said their ELC money was expected to be "coming soon."

"They, like us, are ramping up," Travanty said of the CDC. She says CDC has now doubled the number of samples it has requested from states for its strain surveillance program.

https://www.cbsnews.com/news/covid-19-research-variants-united-states/

Pfizer, BioNTech to limit delays of vaccine shipments to one week

 Pfizer and BioNTech said Saturday (Jan 16) they will limit the delays of their vaccine deliveries to just one week, after fears in Europe that shipments of the jabs could be slowed for up to a month.

The US drugmaker and its German partner "have developed a plan that will allow the scale-up of manufacturing capacities in Europe and deliver significantly more doses in the second quarter," they said in a joint statement.

"As a result, our facility in Puurs, Belgium will experience a temporary reduction in the number of doses delivered in the upcoming week."

Pfizer and BioNTech pledged that deliveries would be back to the original schedule to the European Union from the week of Jan 25, with increased delivery from the week of February 15.

"To accomplish this, certain modifications of production processes are required now." Pfizer had said Friday it would delay shipments of the jabs over the next three to four weeks due to works at its key plant in Belgium.

It said the modifications at the Puurs factory were necessary in order to ramp up its production capacity from mid-February.

In hard-hit Europe, the statement raised concerns that the delays could further slow a vaccine rollout that has already faced heavy criticism.

Six EU health ministers signed a letter to the European Commission on Friday to express "severe concern" over the delivery delays.

The Pfizer-BioNTech vaccine, which was developed at record-breaking speed, became the first to be approved for general use by a Western country on Dec 2 when Britain gave it the go-ahead.

https://www.straitstimes.com/world/pfizer-biontech-to-limit-delays-of-vaccine-shipments-to-one-week

India starts world's largest COVID-19 vaccination drive

 India started inoculating health workers Saturday in what is likely the world's largest COVID-19 vaccination campaign, joining the ranks of wealthier nations where the effort is already well underway.

India is home to the world’s largest vaccine makers and has one of the biggest immunization programs. But there is no playbook for the enormity of the current challenge.

Indian authorities hope to give shots to 300 million people, roughly the population of the U.S and several times more than its existing program that targets 26 million infants. The recipients include 30 million doctors, nurses and other front-line workers, to be followed by 270 million people who are either over 50 years old or have illnesses that make them vulnerable to COVID-19.

For workers who have pulled India’s battered healthcare system through the pandemic, the shots offered confidence that life can start returning to normal. Many burst with pride.

“I am excited that I am among the first to get the vaccine,” Gita Devi, a nurse, said as she lifted her left sleeve to receive the shot.

“I am happy to get an India-made vaccine and that we do not have to depend on others for it,” said Devi, who has treated patients throughout the pandemic in a hospital in Lucknow, the capital of Uttar Pradesh state in India's heartland.

The first dose was administered to a sanitation worker at the All Indian Institute of Medical Sciences in the capital, New Delhi, after Prime Minister Narendra Modi kickstarted the campaign with a nationally televised speech.

“We are launching the world’s biggest vaccination drive and it shows the world our capability,” Modi said. He implored citizens to keep their guard up and not to believe any “rumors about the safety of the vaccines.”

It was not clear whether Modi, 70, had received the vaccine himself like other world leaders to try to demonstrate the shot’s safety. His government has said politicians will not be considered priority groups in the first phase of the rollout.

Health officials haven’t specified what percentage of India's nearly 1.4 billion people will be targeted by the campaign. But experts say it will almost certainly be the largest such drive globally.

The sheer scale has its obstacles and some early snags were identified. For instance, there were delays in uploading the details of healthcare workers receiving the shots to a digital platform that India is using to track vaccines, the Health Ministry said.

Shots were given to at least 165,714 people on Saturday, Dr. Manohar Agnani, a Health Ministry official, said at an evening briefing. The ministry had said that it was aiming to vaccinate 100 people in each of the 3,006 centers across the country.

News cameras captured the injections across hundreds of hospitals, underscoring the pent-up hopes that vaccination was the first step in getting past the pandemic that has devastated the lives of so many Indians and bruised the country's economy.

India on Jan. 4 approved emergency use of two vaccines, one developed by Oxford University and U.K.-based drugmaker AstraZeneca, and another by Indian company Bharat Biotech. Cargo planes flew 16.5 million shots to different Indian cities last week.

But doubts over the effectiveness of the homegrown vaccine is creating hurdles for the ambitious plan.

Health experts worry that the regulatory shortcut taken to approve the Bharat Biotech vaccine without waiting for concrete data that would show its efficacy in preventing illness from the coronavirus could amplify vaccine hesitancy. At least one state health minister has opposed its use.

In New Delhi, doctors at Ram Manohar Lohia Hospital, one of the largest in the city, demanded they be administered the AstraZeneca vaccine instead of the one developed by Bharat Biotech. A doctors union at the hospital said many of its members were a “bit apprehensive about the lack of complete trial” for the homegrown vaccine.

“Right now, we don’t have the option to choose between the vaccines,” said Dr. Nirmalaya Mohapatra, vice president of the hospital’s Resident Doctors Association.

The Health Ministry has bristled at the criticism and says the vaccines are safe, but maintains that health workers will have no choice in deciding which vaccine they will get themselves.

According to Dr. S.P. Kalantri, the director of a rural hospital in Maharashtra, India’s worst-hit state, such an approach was worrying because he said the regulatory approval was hasty and not backed by science.

“In a hurry to be populist, the government (is) taking decisions that might not be in the best interest of the common man,” Kalantri said.

Against the backdrop of the rising global COVID-19 death toll — it topped 2 million on Friday — the clock is ticking to vaccinate as many people as possible. But the campaign has been uneven.

In wealthy countries including the United States, Britain, Israel, Canada and Germany, millions of citizens have already been given some measure of protection by vaccines developed with revolutionary speed and quickly authorized for use.

But elsewhere, immunization drives have barely gotten off the ground. Many experts are predicting another year of loss and hardship in places like Iran, India, Mexico and Brazil, which together account for about a quarter of the world’s COVID-19 deaths.

India is second to the U.S. with more than 10.5 million confirmed cases, and ranks third in the number of deaths, behind the U.S. and Brazil, with over 152,000.

More than 35 million doses of various COVID-19 vaccines have been administered around the world, according to the University of Oxford.

While the majority of the COVID-19 vaccine doses have already been snapped up by wealthy countries, COVAX, a U.N.-backed project to supply shots to developing parts of the world, has found itself short of vaccines, money and logistical help.

As a result, the World Health Organization’s chief scientist, Dr. Soumya Swaminathan, warned this week that it is highly unlikely that herd immunity — which would require at least 70% of the globe to be vaccinated — will be achieved this year.

“Even if it happens in a couple of pockets, in a few countries, it’s not going to protect people across the world,” she said.

https://abcnews.go.com/Health/wireStory/india-starts-worlds-largest-covid-19-vaccination-drive-75291760

SARS-CoV-2 reinfection in 43,000 antibody-positive individuals followed up to 35 weeks

 

View ORCID ProfileLaith J Abu-Raddad,  View ORCID ProfileHiam Chemaitelly,  View ORCID ProfilePeter Coyle,  View ORCID ProfileJoel A Malek, Ayeda A. Ahmed, Yasmin A. Mohamoud, Shameem Younuskunju,  View ORCID ProfileHoussein H. Ayoub,  View ORCID ProfileZaina Al Kanaani,  View ORCID ProfileEinas Al Kuwari,  View ORCID ProfileAdeel A Butt,  View ORCID ProfileAndrew Jeremijenko,  View ORCID ProfileAnvar Hassan Kaleeckal, Ali Nizar Latif,  View ORCID ProfileRiyazuddin Mohammad Shaik,  View ORCID ProfileHanan F. Abdul Rahim,  View ORCID ProfileGheyath K. Nasrallah,  View ORCID ProfileHadi M. Yassine,  View ORCID ProfileMohamed G. Al Kuwari,  View ORCID ProfileHamad Eid Al Romaihi,  View ORCID ProfileMohamed H. Al-Thani, Abdullatif Al Khal,  View ORCID ProfileRoberto Bertollini

doi: https://doi.org/10.1101/2021.01.15.21249731

This article is a preprint and has not been certified by peer review [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.

PDF: https://www.medrxiv.org/content/10.1101/2021.01.15.21249731v1.full.pdf

Abstract

Background: Reinfection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been documented, raising public health concerns. Risk and incidence rate of SARS-CoV-2 reinfection were assessed in a large cohort of antibody-positive persons in Qatar. Methods: All SARS-CoV-2 antibody-positive persons with a PCR-positive swab ≥14 days after the first-positive antibody test were individually investigated for evidence of reinfection. Viral genome sequencing was conducted for paired viral specimens to confirm reinfection. Results: Among 43,044 anti-SARS-CoV-2 positive persons who were followed for a median of 16.3 weeks (range: 0-34.6), 314 individuals (0.7%) had at least one PCR positive swab ≥14 days after the first-positive antibody test. Of these individuals, 129 (41.1%) had supporting epidemiological evidence for reinfection. Reinfection was next investigated using viral genome sequencing. Applying the viral-genome-sequencing confirmation rate, the risk of reinfection was estimated at 0.10% (95% CI: 0.08-0.11%). The incidence rate of reinfection was estimated at 0.66 per 10,000 person-weeks (95% CI: 0.56-0.78). Incidence rate of reinfection versus month of follow-up did not show any evidence of waning of immunity for over seven months of follow-up. Efficacy of natural infection against reinfection was estimated at >90%. Reinfections were less severe than primary infections. Only one reinfection was severe, two were moderate, and none were critical or fatal. Most reinfections (66.7%) were diagnosed incidentally through random or routine testing, or through contact tracing. Conclusions: Reinfection is rare. Natural infection appears to elicit strong protection against reinfection with an efficacy >90% for at least seven months.  

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

The authors are grateful for support from the Biomedical Research Program, the Biostatistics, Epidemiology, and Biomathematics Research Core, and the Genomics Core, all at Weill Cornell Medicine-Qatar, as well as for support provided by the Ministry of Public Health and Hamad Medical Corporation. The statements made herein are solely the responsibility of the authors.

https://www.medrxiv.org/content/10.1101/2021.01.15.21249731v1

Pfizer says second doses of COVID-19 shot on hand, sees no U.S. supply problems

 Pfizer Inc has been holding on to second doses for each of its COVID-19 vaccinations at the request of the federal government and anticipates no problems supplying them to Americans, a spokeswoman said in a statement on Friday.

Pfizer’s comments run counter to a report in the Washington Post that the federal government ran down its vaccine reserve in late December and has no remaining reserves of doses on hand.

“Operation Warp Speed has asked us to start shipping second doses only recently,” the spokeswoman said. “As a result, we have on hand all the second doses of the previous shipments to the US.”

The U.S. Department of Health and Human Services did not respond to requests for comment.

Pfizer has shipped more than 15 million doses to destinations around the United States, primarily from its Michigan facility, and expects to be able to produce around 2 billion doses worldwide in 2021, the spokeswoman said.

The United States has been struggling to administer the shots that have been distributed, however. Only around 12 million of the more than 31 million doses that have been shipped have been administered, according to data from the U.S. Centers from Disease Control and Prevention.

Scattered vaccine shortages were reported on the front lines of the U.S. battle against the coronavirus pandemic on Friday, prompting at least one large healthcare system to cancel a slew of appointments of people hoping to be inoculated.

Earlier on Friday, Pfizer announced there would be a temporary impact on shipments to European countries in late January to early February caused by changes to manufacturing processes to boost output. [L1N2JQ0V3]

Around nine of the 27 governments in the European Union complained of “insufficient” doses at a meeting this week, a participant said.

https://www.reuters.com/article/us-health-coronavirus-vaccine-pfizer-idUSKBN29K2LR