COVID-19 Scan for Apr 15, 2021

News brief

P1 COVID-19 variant more transmissible, may evade cross-immunity

The P1 SARS-CoV-2 variant, which was first identified in Brazil, may be more than twice as transmissible as non-P.1 lineages, and it may lower protective immunity from non-P1 variants 21% to 46%, according to a study published yesterday in Science.

From November 2020 to January 2021, the researchers conducted genomic sequencing on 184 COVID-19 samples collected from the city of Manaus in Brazil's Amazonas state, which has experienced two major COVID-19 surges. Phylogenetic analysis showed that P1 and another lineage, P2, were descendants of lineage B1128, and that P1 probably diverged around Nov 15 after a period of faster molecular evolution. This was 3 to 4 weeks before Manaus, home to 2.2 million people, saw a COVID resurgence.

Within about 7 weeks from late 2020 to early 2021, the fraction of samples classified as P1 increased from 0% to 87%.

The P1 variant is characterized by 17 mutations, including a trio in the spike protein, which is associated with the virus' entry into the human cell. After combining genomic and mortality data, the researchers estimate that P1 may be 1.7- to 2.4-fold more transmissible than non-P1 variants, and by Feb 7, the estimated reproduction number was 0.5 for P1 and 0.1 for non-P1 lineages. P1 may also be able to evade 21% to 46% of protective immunity from previous infection with non-P1 lineages, according to the researchers.

Data from all COVID-19 samples during P1's emergence suggest the variant produces higher viral loads (with 1.43 to 1.91 lower cycle threshold values). Similarly, while mortality rates appear to be 1.2 to 1.9 times higher in association with P1's dominance, the researchers do not know how much this is because of the city's overburdened healthcare system.

"Studies to evaluate real-world vaccine efficacy in response to P.1 are urgently needed," the researchers write, adding that P1 is in more than 36 countries. "We note that neutralisation titers represent only one component of the elicited response to vaccines, and that minimal reduction of neutralisation titers relative to earlier circulating strains is not uncommon."
Apr 14 Science study

Dogs able to sniff out COVID-positive urine, saliva in pilot study

Nine dogs were able to sniff out COVID-positive urine and saliva samples in a proof-of-concept study published yesterday in PLOS One, but the researchers note that a lack of sample diversity made it difficult to tell how generalizable the training was.

Training was conducted with a scent wheel that had various scents at the end of the spokes. First the dogs were trained to detect a distinctive scent with a universal detection compound. Then they moved onto COVID-positive and -negative urine samples, all treated so the virus was inactivated, and lastly, treated saliva samples.

Across the 3 weeks of training and multiple trials, the researchers mixed positive samples from 14 children and 5 adults and used both heat- and detergent-based inactivation techniques. None of the dogs had done medical detection work prior.

During training, accuracy for heat- and detergent-treated urine was 94%, but trials introducing variables showed accuracy ranging from 11.1% to 100%, where any change in behavior was considered a reaction. The most successful rates were when dogs detected detergent-treated urine samples mixed from previous samples they had smelled before and when dogs were presented with a novel COVID-positive saliva sample and told to find another positive saliva sample. The dogs were least accurate when they tried to find heat-treated, COVID-positive urine among completely novel samples.

Excluding the trial that led to 11.1% accuracy, the cumulative accuracy was 92.5%. The researchers note that the low sensitivity rates (11% to 71%) could be partially explained by their strict definitions: Any time the dog passed by a positive sample with no reaction, it was counted as a miss.

"The training utilized in this study did not result in documented generalization of a SARS-CoV-2 positive odor profile, despite dogs showing impressive discrimination between positive and negative samples," the researchers write, noting that the dogs were able to discern individual patients over time. "This suggests that either the number of samples, or the number of sample presentations, though likely both, need to be better suited for not just discrimination but also generalization."
Apr 14 PLOS One study

News Scan for Apr 15, 2021

News brief

Study: MERS antibodies persist up to 6 years

A study of antibodies in 48 people in Saudi Arabia who survived their MERS-CoV infections found that some neutralizing antibodies persisted 6 years, a Saudi-led team reported yesterday in Emerging Infectious Diseases.

Scientists are closely watching for new information about the durability of antibody response to coronavirus infections, given that three diseases involving them have emerged in humans over the past couple decades: SARS (severe acute respiratory syndrome), MERS-CoV (Middle East respiratory syndrome coronavirus), and now SARS-CoV-2, which causes COVID-19.

For the study, researchers looked at blood test findings in 48 MERS survivors from five hospitals in Jeddah and Riyadh. Illnesses ranged from mild to severe. Convalescent blood samples were collected at 2 to 3 years for 57.1% of the patients, 4 years postinfection for nearly 24.5%, and 5 to 6 years for 18.4%. ELISA testing was performed on 45 samples, with microneutralization assays done on 49.

Antibodies specific to MERS-CoV were detected for 6 years after infection, including 100% of those who had moderate or severe disease and 50% of those who had mild disease. Some people who had mild or moderate disease had negative ELISA results. The authors said the results suggest durable immunity against the virus, and they wrote that future studies would be useful to determine if the antibody levels would protect against infection.
Apr 14 Emerg Infect Dis study

In other MERS developments, the World Health Organization (WHO) yesterday posted an overview of seven cases in Saudi Arabia reported so far this year, which were noted in earlier updates from the country's health ministry. Four patients are from Riyadh, and Jeddah, Al Ahsa, and Mecca regions each reported one case. Four patients died.

Ages range from 46 to 84, and all but one of the patients are male. All had underlying health conditions. None had contact with other known MERS-CoV patients and none were healthcare workers. Three had exposure to camels or camel milk, which are known risk factors.

The WHO said the cases lift the global total to 2,574 confirmed cases, including 886 deaths.
Apr 14 WHO update

Mali reports first H5N1 avian flu outbreak in poultry

In the latest highly pathogenic avian flu outbreak developments, Mali reported its first H5N1 outbreak in poultry, Hungary reported another H5N1 outbreak in poultry, and Russia reported another H5N5 detection in wild birds, according to the latest notifications from the World Organization for Animal Health (OIE).

Mali officials detailed three outbreaks that began on Mar 12, affecting a layer farm in Sikasso region, a layer farm in Koulikoro region, and a backyard farm housing exotic chickens and other poultry near Bamako, the country's capital. All are in southern Mali.

Taken together, the virus killed 39,860 of 50,150 susceptible birds, and the rest were culled to control the spread of the virus. So far, the source of the virus hasn't been identified. Other African nations have reported recent H5N1 detections, including Nigeria and Niger.

Hungary reported an H5N1 outbreak at a turkey breeding farm in Hajdu-Bihar County in the east. The outbreak began on Apr 9, killing 2,650 of 11,769 susceptible birds. And Russia's latest H5N5 outbreak was in pelicans at a nature park in Astrakhan oblast in the southwest. The outbreak began on Mar 29, killing 99 birds.
Apr 15 OIE report on H5N1 in Mali
Apr 13 OIE report on H5N1 in Hungary
Apr 14 OIE report on H5N5 in Russian wild birds