Readiness is All: Replikins Give Advance Warning of Zika Outbreaks

On February 23, 2017, the first day of the First International Zika Conference, held in Washington, DC, Samuel Bogoch, MD, PhD, professor of Emergency Medicine at Boston University School of Medicine, chairman at Replikins LLC, Foundation for Research on the Nervous System, explained to a room full of interested conference-goers how Replikins, a class of peptide sequences, can be used to give advanced warning of outbreaks and their cessation.

Replikins are a group of gene peptides that are associated with rapid replication; they are 7 to 50 amino acids long and are sequences that are “specific to amino acids, and spaces between” that are “identified and counted by an automated process.” Perhaps one of the most important takeaways that Dr. Bogoch drove home was that, “Replikin concentration increases before outbreaks and decreases before cessation.”

In his presentation, Dr. Bogoch outlined that Replikins can be visualized in three ways:

1. 3D x-ray diffraction
2. Mean and standard deviation of the concentration (Replikin count)
3. By plotting individual specimen Replikin counts

To illustrate the different ways, he provided the audience with three examples. The first depicted how Replikins can be visualized through 3D x-ray diffraction. For the H1N1 pandemic, Dr. Bogoch showed how this method could illustrate the H1N1 HA gene increasing before the 2009 outbreak actually occurred. Dr. Bogoch shared that this was probably the first local "pandemic that was tracked in real-time from its first signs of x-ray diffraction through to its high point in 2009.” He said, “So, we actually had a few years of warning of this coming.”

Dr. Bogoch went on to explain that this visualization, or “visual imprint,” is supported by the Replikin count which was depicted to increase from 3.2 in 2001, to 5.5 in 2005, to a whopping 10.1 in 2009. 3D x-ray diffraction is “one way to visualize the Replikin’s peptides as they increase in number and spread over the surface of the gene,” Dr. Bogoch said.

The second example consisted of the mean and standard deviation of the concentration (Replikin count) pertaining to hand, foot, and mouth disease (HFMD) outbreaks in China.

The last example plotted H1N1 HA individual specimens in Mexico and New Mexico according to year. “You can see the beginning pre-outbreak, you have a rise in the Replikin count from about 3 up to 8 and that was the one that got a little bit of attention because we predicted a year before the outbreak of the pandemic that it was going to occur and it did occur,” Dr. Bogoch explained.

He then showed the audience an example plotting the individual specimen Replikin counts of Ebola in 2013-2014 and how they helped to predict the 2014-2015 outbreak and cessation. He stressed that what was being seen was a “very different pattern” than the H1N1 HA visualization. With Ebola, a huge increase in count was seen in 2013, going from 1 or 2 to 25. Then, in October 2014, it significantly dropped; the researchers investigated if the drop, was, in fact, real. They found that the drop was not only real, but it persisted all the way through 2013, 2014, and 2015, “and it’s still going on.” He explained, “Ebola is therefore having a break for a moment, but when it starts to get active again, we will be able to see it.”

Dr. Bogoch proceeded to compare the two plotted visuals of H1N1 outbreak in Canada and Ebola outbreak in Africa 2014 and visually demonstrated two different time-course patterns of gene mutation and molecular evolution. Ebola illustrated the “time-course I” pattern in that there was a “rapid” increase in Replikin count and gene mutations (at p<.001) “within 1-2 years in advance of the clinical outbreaks with high mortality, (40-70% in this case), followed by rapid cessation of gene change within the year of the outbreak, followed promptly by rapid cessation of the outbreak, and no recurrence within two years.” The H1N1 influenza pandemic of 2009-2010 illustrated the “time-course 1” pattern in that there was a gradual increase in Replikin count/gene mutations (at p<.001) “over a period greater than two years in advance of the clinical outbreak, followed by gradual cessation of both the gene change and of the clinical outbreak, followed by annual endemic recurrences.”

“You may think that this has nothing to do with Zika, but what it does do is show us that if you get enough samples and they are done carefully—year by year&mdash;and you do the Replikin counts, the rise in Replikin counts are followed by a rise in the number of cases of this disease,” Dr. Bogoch stated.

Zika is following more of a time-course 2 pattern, according to Dr. Bogoch. He explained, “We don’t expect it to have a sudden drop…Despite the slight decline globally, Brazil Replikin counts continue to increase, indicating possible [a] repeat epidemic in Brazil in the coming summer season.”

Dr. Bogoch feels that Replikin technology reduces the pathogen’s advantage of completely surprisng the world once an epidemic hits. “You realize that for centuries we have shown surprise any time any old outbreak happens; it’s a chronic repeat. This, of course, keeps the pharmaceutical companies very busy because they say ‘Oh, you’re frightened by the outbreak? Just give us some money and we’ll make you some vaccine.’ The vaccine always comes just about when the epidemic is leaving. So, hopefully, we’ve got a bit of advanced notice here and it provides more time for pre-outbreak public health responses,” stated Dr. Bogoch.

In an updated abstract, Dr. Bogoch shared that Zika gene mutations are continuing to increase. In fact, they “markedly” increased in 2016 “as evidenced by the appearance of new Zika Replikin Strains.” Between 2000 and 2010, there were only 3 Zika strains and from 2010 to 2015 there were 12 different strains that were detected by different methods. However, as of December 4, 2016, 49 Zika strains were detected. Furthermore, as of February 20, 2017, 54 Zika Replikin Strains have been detected. “This means that we are in a very active heterogeneous time of mutation because you have to have mutation to make a structured change in the gene and when you see that, you know you’re in for big trouble if your vaccine is based upon genes from the years before 2016,” according to Dr. Bogoch. He emphasized, “As the increase in mutations increases, so does the risk of your vaccine being outdated.”

With this information, researchers will be able to track Zika and predict when potential outbreaks will occur, thus providing more time for pre-outbreak public health response as well as the development of “made-to-measure” vaccines.

Dr. Bogoch concluded with a quote from Shakespeare’s Hamlet: “The readiness is all.” He explained, “And the readiness is all. I know that we’re all concerned with that, but now maybe we have some tools to add to our knowledge of what’s happening while we wait for the next step.”

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First International Conference on Zika Virus

PRESENTATION

Session 1: Zika Epidemiology

Specific Zika Virus Gene Structures, Replikins, Give Automated Quantitative Advance Warning of Outbreaks and Their Cessation