COVID-19 Scan for Dec 16, 2021

News brief

Study finds low Omicron antibody response with COVID-19 vaccines

Only 20% and 24% of Pfizer/BioNTech COVID-19 vaccine recipients in a Chinese study had detectable neutralizing antibodies against two isolates of the highly transmissible Omicron (B.1.1.529) variant, while recipients of the Coronavac vaccine had no antibodies against either isolate.

The study, published today in Clinical Infectious Diseases after appearing on a preprint site 2 days ago, was led by University of Hong Kong researchers, who isolated Omicron strains HKU691 and HKU344-R346K from patients.

Only 20% and 24% of Pfizer vaccinees had antibodies against HKU691 and HKU344-R346K, respectively. None of the Coronavac recipients had antibodies against either strain. Among Pfizer recipients, the geometric mean antibody neutralization titers (GMT) of the Omicron isolates were 35.7- to 39.9-fold lower than those against the original 2020 strain.

The GMT of both isolates were significantly lower than those against the Beta (B1351) and Delta (B1617.2) variants, and there was no significant differences in the GMT of the Omicron variants. Coronavac is made by Beijing-based Sinovac and is the world's most-used COVID vaccine, accounting for almost half of the 8.6 billion global doses administered to date.

"Omicron variant escapes neutralizing antibodies elicited by BNT162b2 [Pfizer] or Coronavac," the authors concluded. "The additional R346K mutation did not affect the neutralization susceptibility. Our data suggest that the Omicron variant may be associated with lower COVID-19 vaccine effectiveness."
Dec 16 Clin Infect Dis study

Internal review shows first CDC COVID-19 tests inaccurate, contaminated

The first COVID-19 tests distributed by the US Centers for Disease Control and Prevention (CDC) were prone to false-positives due to flaws in assay design and contamination in assay components, according to an internal review of the tests published yesterday in PLOS One.

After the first SARS-CoV-2 genomic sequence was obtained from a patient in Wuhan, China, on Jan 12, 2020, the CDC began to develop a Real-Time RT-PCR Diagnostic Panel to identify the virus. The first tests were distributed to public health labs on Feb 5. Reports of false-positives soon followed.

The tests were composed of a diagnostic panel targeting three viral nucleocapsid gene loci (N1, N2, and N3 primers and probes), of which the N1 component was contaminated, allowing for more false-positives (2%).

CDC scientists were able to fix the N1 component, but N3 eventually had to be removed from the diagnostic panel because of a design flaw and was not included in the test that received emergency use authorization. According to a press release on the study, two molecules in the N3 probe frequently bound to each other in the absence of any virus, triggering a false positive test results.

"We conclude that flaws in both assay design and handling of the 'bulk' material caused the problems with the first lot of the 2019-nCoV Real-Time RT-PCR Diagnostic Panel," the authors wrote.
Dec 15 PLOS One study
Dec 15 PLOS press release

News Scan for Dec 16, 2021

News brief

DRC's 13th Ebola outbreak declared over

The Democratic Republic of the Congo (DRC) today declared the end of its thirteenth Ebola outbreak, given that two 21-day incubation periods have passed since the last patient was discharged from treatment, the World Health Organization (WHO) African regional office said today.

There were 11 cases, 8 of them confirmed and 3 probable, and 6 people died from their infections. The outbreak was declared on Oct 8 and was focused in North Kivu province's Beni health zone, which was one of the hot spots in the country's large 2018 outbreak.

Genetic sequencing from the first case confirmed in the outbreak suggested that the outbreak may have been a flare-up related to the earlier outbreak, perhaps due to persistent virus in a survivor.

The WHO said a vaccination campaign, launched just 5 days after the first case was found, reached more than 1,800 people and included the DRC's first use of Merck's Ebola vaccine in its fully licensed form, which made rollout less cumbersome compared to when it was used on a compassionate-use basis.

Matshidiso Moeti, MBBS, who directs the WHO African regional office, praised the DRC's swift response. "During this outbreak, the Democratic Republic of Congo was able to limit widespread infections and save lives. Crucial lessons are being learned and applied with every outbreak experience," she said, adding that the WHO deployed experts, supplies, and funds to help control the outbreak.

In Beni, outbreak responders faced familiar challenges that hampered the large previous outbreak, including volatile security situations. Health officials will maintain illness surveillance, given that occasional flare-ups are expected following major outbreaks.
Dec 16 WHO statement

UK's DEFRA: Poultry threats remain from high-path avian flu

Highly pathogenic avian flu outbreaks involving poultry and virus detections in wild birds continued at a brisk pace in the United Kingdom and Europe in the first part of December, the UK's Department for Environment, Food, and Agriculture (DEFRA) said in its latest risk assessment.

Fifteen more H5N1 outbreaks have been reported in Britain since DEFRA's last update on Dec 6. Also, Belgium, France, Germany, Hungary, Ireland, Poland, and Russia reported more highly pathogenic H5N1 outbreaks in poultry, and Ireland reported H5N1 at two more locations.

Avian flu detections in wild birds continue to be reported in northwestern Germany, as well as coastal parts of the Netherlands, Luxembourg, Denmark, and Sweden. Greece and Portugal recently reported their first H5 detections of the season in wild birds.

DEFRA kept the risk of exposure to poultry as medium where good biosecurity is in place and at high for locations that have biosecurity lapses.
Dec 13 DEFRA update