Covid-19: A deep dive on community transmission

How do researchers determine where infections originate?

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Image Credit: A computer generated representation of COVID-19 virions (SARS-CoV-2) under an electron microscope. Image credit: Felipe Esquivel Reed

There has been a recent rise in coronavirus cases across the UK, including in York. Due to a 15-20 day time lag between infections and treatment, this has led to a corresponding increase in hospitalisations and deaths. But one thing that has also corresponded to it is the decrease in daily number of vaccinations. Looking at the data, it seems the vaccination rates in the UK have plateaued from 752,308 getting their first dose and 91,977 people getting their second dose on 20 March to just 39,966 and 23,723 respectively. However, This plateau is of concern since only 67.9 percent are fully vaccinated, whereas 79.4 percent of the population have received their first dose. Furthermore, despite the high percentage of the UK population being vaccinated, there still seems to be a rise in cases of the delta variant in particular.

A study done by Imperial College London and the National Institute of Health Research published in the Lancet in October1 involved investigating the effect of vaccinations on the viral load in patients, as well as its effect on community transmission of the delta variant of Covid-19. The paper noted a previous study’s finding that vaccinations are found to be effective in reducing household transmission of the alpha variant by 40-50 percent and are also effective in reducing viral load compared to their unvaccinated counterparts. Though there have been indications that vaccinations help in reducing the risk of hospitalization and death for delta variant infections, many highly vaccinated countries have still reported high infection rates. Considering this, the group decided to study the effect of vaccinations on delta variant infections and community transmission and compare with the alpha and pre-alpha variants.

The study involved two groups: those who tested positive for the pre-alpha and alpha variants, and those testing positive for the delta variant. Household and non-household contacts were identified by NHS Track and Trace. Each contact took daily tonsil swabs and submitted questionnaires on their health characteristics. The vaccination status of the person who is transmitting the disease and their contacts were recorded: fully vaccinated individuals were considered to be those who received their second dose at least seven days before the study, and partially vaccinated individuals were those who received their second dose within seven days of enrolling in the study. Viral samples were also collected from individuals with less severe infections in order to provide data on the effects of the degree of infection on the transmission potential of vaccinated individuals.

A quantity called the secondary attack rate (SAR) was calculated for the household contacts and participants divided by the vaccination status of their contact. This helps to quantify how infectious a contact is, and how well this links to whether or not they were vaccinated.

A second method used was a kinetic analysis, which is conducted using a computer model. This involved detecting differences in the peak viral load and its growth and decline rates in participants. This was then analysed to classify participants into four groups: those with the pre-alpha and alpha variants, and those with delta who were both vaccinated and unvaccinated. This type of hierarchical grouping makes it much easier to zoom in on interesting differences that could be caused by vaccination status.

One of the prominent findings was that there was no difference in peak viral load among the variants or among the different vaccination status of the positive patients, though they found that the viral load does increase with age. Additionally, they also found that the viral load decreases faster for alpha and pre-alpha variant infections than for delta. The rate of viral load decline is a quantitative way to measure the effectiveness of the immune system. A higher rate of viral decline means that the immune system is better equipped to fight that particular variant. This suggests that our current vaccines are better able to train the immune system to fight the pre-alpha and alpha variants than they are to target delta Moreover, their study has provided first hand evidence that with each variant or vaccination group, the viral growth rate increases with peak viral load, meaning that more widespread infections grow faster, which fits our understanding of how viruses multiply. However, they also found that with a higher peak,viral decline rate can also increase, suggesting our immune response is the most important factor in fighting off infection.

Remember the secondary attack rate (SAR)? Unfortunately, the study did not find a significant difference in SAR between fully vaccinated index cases and unvaccinated cases (23 and 25 percent respectively, which indicates that vaccinated individuals still transmit the virus, especially in households, which are prolonged and close settings causing larger exposure to the virus. The authors do cite similar studies that have been done in other countries that also calculated SAR and it’s relation to peak viral loads. However, those studies only used certain groups based on a certain age, and in some cases only considered hospitalised patients. This study in particular has gathered more participants to include a community transmission setting, and thus has provided more useful insight into how the virus moves throughout the spaces we inhabit.

This study overall provides evidence to explain the rise in cases despite the higher rate of vaccinations. The authors have thus suggested that vaccinations alone cannot prevent transmission of the delta variant in household settings, further suggesting that booster programs and offering the vaccination to more groups, e.g. teenagers is needed. Additionally, the low vaccination rates in recent days is a likely explanation for increasing hospitalisations. The good news though, is twofold: the evidence that vaccines improve patient outcomes is indisputable, and the NHS has established a well-oiled machine of immunisation-delivery, and all we need to do is make more use of it.



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