Coronavirus disease 2019 (COVID-19) initially emerged in Wuhan, China, and rapidly spread to nearly every country in the world, causing over five million deaths and widespread economic crises. Initially, many governments relied on extensive restrictions to help curb the rapid transmission of the disease, including mandatory face masks, the closing of public spaces, and even full lockdowns/stay-at-home orders.
Study: Active epidemiological investigation on SARS-CoV-2 infection caused by Omicron variant (Pango lineage B.1.1.529) in Japan: preliminary report on infectious period. Image Credit: judyjump/Shutterstock
When a series of vaccines were created and mass administration programs allowed developed countries to immunize the vast majority of their population, most of these restrictions were dismantled. Unfortunately, a series of variants emerged in the latter half of 2020 through 2021, displaying increasingly worrying traits. Mutations altered the shape and structure of certain proteins, reducing vaccine efficiency or increasing transmission rates. The most recent of these is named Omicron, of Pango lineage B.1.1.529, which has gained extensive media attention due to a rapid rise in cases and the number of significant mutations it carries.
Researchers from the National Institute of Infectious Diseases have been investigating the Omicron epidemic in Japan and have recently released an early report on the infectious period of the disease.
Most variants of concern (VOCs) carry mutations in the spike protein. This transmembrane, homotrimeric protein is key to the pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It contains two subunits that must be split by a host cleavage protein, S1, and S2. S1 contains a receptor-binding domain (RBD) that binds to angiotensin-converting enzyme 2(ACE2) to permit viral cell entry, while S2 is responsible for mediating membrane fusion.
Most vaccines target the spike protein, so any mutations that significantly change the structure can allow for at least some immune evasion. Many variants show different proportions of conformations of the spike protein: each one of the three monomers can take one of three positions, ‘up,’ ‘down,’ or a rare intermediate position. Facing down makes it more difficult for antibodies to bind to the spike protein and reduces ACE2 binding.
Several important effects of the mutations in Omicron have already been discovered – a mutation near S2 makes it more difficult for the host cleavage protein to split the subunits, reducing membrane fusion, and another changes the proportion of conformations of the proteins, with some showing a monomer in the rare intermediate position.
The researchers attempted to investigate Omicron cases with the cooperation and mutual assistance of several different medical facilities in Japan. They were primarily investigating viral shedding – one of the main transmission causes. Eighty-three respiratory specimens were examined from 19 vaccinated individuals and two unvaccinated individuals. All of these cases were confirmed by SARS-CoV-2 RNA quantifications using quantitative reverse transcriptase-polymerase chain reaction (rtPCR) and virus isolation tests, with the date of specimen collection or the beginning of symptoms set as day zero.
The highest amount of viral RNA was collected between days three and six and then generally tended to decrease over time, with the greatest decrease seen after ten days. This is supported by similar findings exploring infectivity regarding isolation, which found that most individuals who isolate are virus-free by day 10. Positive virus isolation results also confirmed this finding, and the researchers conclude that vaccinated individuals who contract Omicron are unlikely to shed infectious virus after ten days.
The information these researchers have gathered could be very useful for epidemiologists and public health policymakers. As cases continue to rise and the Omicron variant spreads through highly vaccinated populations, this report could be used to guide future isolation and quarantine procedures, especially as healthcare services struggle with labor shortages due to isolation. While the sample size was relatively small, it is supported by multiple similar studies with equivalent findings.