Vaccines and variants: What you need to know

Conversations with Data: #67

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Welcome to our latest Conversations with Data newsletter.

In this week's Conversations with Data podcast, we spoke with vaccinologist Dr Melvin Sanicas about the new COVID-19 variants from South Africa, Brazil and the United Kingdom. He explains to us how epidemiological surveillance works and how these new variants could impact the current vaccine rollout programme.

You can listen to the entire podcast on Apple Podcasts, Google Podcasts, Spotify, or SoundCloud. Alternatively, read the edited Q&A with Dr Melvin Sanicas below.

What we asked

Talk to us about these new variants from South Africa, Brazil and the United Kingdom. How do they come about?

The appearance of variants is not at all surprising because viruses mutate. That's what they do. When a virus particle enters a host cell, it converts that cell into a viral factory, churning out thousands of new virus particles in a relatively short period of time. And because replication is not perfect, there will be some changes, some mutations. Many of these mutants may be different genetically from the original virus, but not exhibit any biological important differences. Others can be inferior, which means that mutations made these viruses less able to replicate.

In a few cases, however, the mutations may confirm what's called a selective advantage. This means that a particular mutant might be able to infect a person more readily or replicate more inside the body, or even just leave a person's body more easily. These types of changes make a virus more likely to survive and reproduce, which can be worrying in the case of more dangerous viruses.

So in general, coronaviruses mutate less rapidly than the flu, for example, or HIV. But SARS-CoV-2 has been mutating throughout the pandemic. In fact, early in the pandemic, I think it was around April or May last year, one particular variant referred to as the D614G, quickly replaced the initial SARS-CoV-2 strain throughout the world. And this contains a change in the virus spike protein that allows the virus to be more easily transmitted from host to host. And because of this biological difference, the variant spreads rapidly. But if you are wearing masks properly in the right kind of mask, washing your hands regularly and keeping your distance from people, this variant cannot infect you.

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Talk to us about how viruses are sequenced. What does that involve?

A genome is an organism's genetic material. It's essentially the instruction manual which contains all the information needed to make and maintain the virus. Virus genome sequencing is essential in understanding the spread and evolution of SARS-CoV-2. So how is this done? I'm not involved in a genomic sequencing lab at the moment. The last time I did this was several years ago for a different pathogen. But basically, someone swabs the patient's nose and we pull genomic material out of the sample using a little handheld DNA sequencer. This is typically smaller than a smartphone and connects directly to a laptop via a USB.

The data analysis software then does the sequencing of the genome and uploads the sequences directly into international databases. These databases can be accessed by people in the viral genomics community. This means scientists anywhere in the world working on viral genomics can have access to the widest array of data as possible. And by looking at the genomic sequence of the virus, we can have an idea where their version of the virus came from. We can also understand how the virus is spreading because the genomic sequence looks a little different as the virus mutates and spreads in different geographic areas. We can even tell if this virus is from Europe, Wuhan or even Singapore, for example.

Not every country conducts genomic surveillance on a regular basis. Why is that?

I think it's really more of a question of resources. For instance, should they increase genomic sequencing capacity or buy more PPE or buy more vaccine? And this is because genomic sequencing is considerably more expensive than a COVID diagnostic test, for example. It's not feasible to isolate every positive COVID-19 case and screen for the new variant. It's important for researchers to work with local clinical epidemiologists to build a monitoring strategy. If all countries with high transmission do genome sequencing or do more genome sequencing than what they are doing at the moment, I'm sure each country will be able to identify a new variant.

How do these new variants impact the current vaccines?

Changes in the spike protein of the virus could potentially alter the effectiveness of the newly developed vaccines. Most of the major vaccines in development at the moment focus on the spike protein. Mutations in the gene encoding for the spike protein could, of course, alter the structure, make some changes. Studies have been designed to explore the effectiveness of the existing vaccines against the new variant. Pfizer and Moderna released preprints from their studies recently. They showed that even though there are some reductions in neutralisation, overall, the antibodies produced by vaccines using Pfizer and Moderna are still able to neutralise the virus with these new variants.

The Johnson & Johnson vaccine is a one-dose shot. Should countries be opting for that one instead of the other two-dose vaccines?

Governments should opt for whatever vaccine has been reviewed and approved by the national regulatory authorities. If we want to stop the pandemic, we need to scale up vaccination efforts now. If this vaccine from Johnson & Johnson has an efficacy similar to the Oxford-AstraZeneca vaccine, with only one dose, surely it's a great addition to the covid vaccine family. But realistically, it's not a matter of choosing one over the other because no single manufacturer can produce doses for the whole world. Some will have to use vaccine A and some will have to use vaccine B, others will have to use vaccine C and so on and so forth. And every single day we wait for vaccine J to come into the picture is an opportunity for the virus to spread, mutate and create more variants.

And as an example, the full effects of Pfizer's two-dose vaccine are only expected to be seen in two weeks after the second dose. But recent data from Israel has already shown that there is a significant drop in infections even before this point. They have seen a 60 percent reduction in infections three weeks after the first doses were given. So I think we have to roll out vaccines as early as possible and not wait for the perfect vaccine.

What should journalists be mindful of when interviewing different experts and scientists about COVID-19?

I understand why everyone is saying things about the pandemic or the virus because we are all affected and we are entitled to an opinion. But if people's opinions are not based on what they were trained to do, or based on their experience, these opinions add to the confusion. And people who are not doctors or scientists might think that all doctors or scientists are COVID experts. But this is not the case.

For immune system questions, of course, you have to ask immunologists. For the virus itself, you have microbiologists and more specifically, the virologists. For managing COVID-19, you have to speak to infectious disease specialists for questions on community transmission. For public health advice, you have the epidemiologists and public health physicians. And it's also good to know within epidemiology itself, there are specialisations. For COVID-19, we need to speak to those with infectious disease epidemiology expertise because not all epidemiologists are the same.

How do vaccinologists like yourself fit into the picture?

Vaccinology is a subspecialty of microbiology. It's a combination of immunology, microbiology, infectious diseases, public health and immunology. We've studied bits and pieces of these different subspecialties of medicine. We can understand what's happening and we can have a bigger picture of of the vaccines, of the various treatments and even public health.

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Our next conversation

Our next Conversations with Data podcast will feature Denise Malan, interim executive director of IRE, a US-based nonprofit membership association for journalists. She was a newspaper journalist for more than a decade, using data to shed light on local issues in government, schools, the environment and other beats. She will talk to us about the virtual NICAR 2021 event happening on March 3-5.

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As always, don’t forget to let us know what you’d like us to feature in our future editions. You can also read all of our past editions here.


Tara from the EJC Data team,

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