by Thomas Hopp
Glu-Val-Lys-Ser-Glu-Arg
Ser-Arg-Arg-Gly-Glu-Asn
His-Gly-Asp-Arg-Ile-Glu
“These are the top picks of the Hopp and Woods algorithm for the G1 insertion,” he said. “The most surface-exposed parts of the protein.”
“The antibody attachment-points?”
“Exactly. And I notice they are also the segments that do not match the bird sequences.”
“So Holloman vaccine immunizes against the unknown parts, not the bird parts?”
“Very good, Fin. Now, I’m going to play a hunch.”
He typed:
protein match versus human proteome
As the computer worked again, he explained. “This time, I’m not asking the computer to try to match DNA to DNA. That’s what Beryl tried, and she failed to find anything. Sometimes, however, a direct protein-to-protein match can find similarities that might otherwise be missed. The computer is checking the antigenic sites against every protein in the human genome. That’s about 30,000 proteins, so give it a while.”
“I’m confused,” I said. How can the DNA codes not match, but the protein codes match? Don’t DNA and RNA code for protein?”
“Answer: yes,” McKean replied. “But DNA encodes proteins in a redundant way. Multiple DNA codes exist for each amino acid. For instance, the amino acid valine is encoded in DNA by any of four triple-letter sequences: GTT, GTC, GTA or GTG. The amino acid serine is encoded by any of six different triplets. So, you see, any given amino acid can be specified by entirely different DNA sequences.”
We waited for several minutes until the screen display changed. Now the three original antigenic segments were aligned with three more:
MATCHES FOUND WITH P410:1910
GluValLysSerGluArg 5 of 6 amino acids match
GluValLysSerThrArg
SerArgArgGlyGluAsn 5 of 6 amino acids match
SerArgArgAlaGluAsn
HisGlyAspArgIleGlu 4 of 6 amino acids match
HisGlyAspArgLeuGln
“Hah!” McKean exclaimed with a bright smile. “I knew it. Look carefully, Fin. Only one amino acid is different between each of those sequence pairs - except the third pair, which has two amino acid differences.”
I scratched my head. “So, are they the same, or different?”
McKean grinned with the pleasure of scientific discovery. “I assure you, although they differ slightly, we have got a solid antigenic match. Antibodies against the first member of each pair will most assuredly cross-react and bind the second. But let’s see why the DNA searches didn’t pick this up.”
He keyed in:
dna code
The display quickly altered to show the DNA that had encoded the protein segments:
GAAGTTAAATCCGAACGT 7 of 18 code letters match
GAGGTAAAGATTACCAGG
TCAAGACGCGGTGAAAAC 6 of 18 code letters match
AGTCGTAGGCAAGAGAAT
AGTGGAGATCGCATTGAG 8 of 18 code letters match
TCCGGTGACAGACTGGAA
“See that?” McKean said with pride. “Much less DNA match, compared to the strong amino-acid matches. The DNA code letters are identical less than half the time in all cases, and only one-third of the time in the second pair of sequences. In DNA searching, a one-quarter match happens by random chance, so these weak matches are not far above random. On the other hand, the amino-acid matches are almost perfect in two cases and no worse than three-quarters in the other case. That’s quite high. So what we have is an example of weak DNA matches coding strong amino-acid matches.”
“It’s almost as if the virus wanted to trick the computers.” I remarked.
“An interesting concept,” McKean said with the forbearing smile he wears when I overinterpret scientific data. “But viruses aren’t capable of wanting or tricking. And now we know the truth. G1’s inserted sequence is definitely related to a human protein even though its DNA code has shifted until it can’t be computer-matched.”
“And can only be McKean-matched?” I asked.
He smiled the subdued smile he wears when flattered. “Think of it that way if you like, Fin. And now let’s see which protein we’ve matched up with.” He keyed:
abstract P410:1910
The screen quickly changed to give details of the protein in question:
Human brain protein gp91
Protein Family: NCAM related
Tissue distribution: Frontal cortex and hypothalamus
Cellular location: neuron cell surface
McKean’s smile faded. “My God!” he murmured. “An antibody attack on that would be…”
“Fatal?”
“Answer: yes!”
Within a minute, McKean had reached Kay Erwin at her office on a video call.
She said, “I was just going to call you. We’ve got the results from the Pathology Department for Pete Whitehall’s brain.”
McKean immediately said, “Severe damage to the frontal cortex and hypothalamus.”
“How could you know that?” Erwin asked, astonished. “I just got the results myself.”
“Ever heard of gp91?” McKean asked her.
“You’re the protein expert.”
“Gp91 has me quite worried,” he said. “It’s found in the human frontal cortex and the hypothalamus, and as we have just discovered, the Holloman vaccine carries a copy of something like it in its G1 protein component.”
“You’re making me nervous, Peyton. What are you getting at?”
“I just figured out that the G1 insertion is related to the NCAM family of proteins. The acronym stands for Neural Cell Adhesion Molecule. If you need a way to stick a virus to cells of the nervous system, look no further. Binding to nerve cells is what that molecule is all about. Furthermore, NCAM proteins tend to form homodimers.”
“Homo - ?”
“Homodimers are a way of binding that depends on two identical molecules attaching to each other, as opposed to heterodimers, where two non-identical molecules combine. NCAM forms homodimers, that is, NCAM-to-NCAM connections. Apparently this virus has coopted a piece of an NCAM protein to enable its nerve cell binding.”
“Now you’re terrifying me, Peyton. A virus that’s using a part of ourselves against us?”
“Precisely. Now, let’s consider what may happen when we immunize with a vaccine containing the G1 protein’s NCAM portion. The patients’ immune responses may include antibodies that target not only the viral NCAM, but also the normal gp91 NCAM in their own brains.”
“Tell me it isn’t true, Peyton.”
“I wish I could.”
Kay wore as bleak an expression as I have ever seen on her. She asked, “What’s the worst-case scenario for that sort of cross-reaction?”
McKean leaned back, knit his fingers behind his head, unfocussed his eyes, and allowed his prodigious imagination to run along the path of his logic. “The antibodies that cross-react with gp91 might destroy exactly the same portions of the brain that the virus destroys. In that case, you would expect - ” A horrified look came across even his normally cool face. “You would expect a vaccinated subject to exhibit the very same symptoms that the virus causes!”
“Oh, my God!” Erwin gasped. “The Holloman vaccine is already being mass-produced. What percentage of people might get the disease from it?”
McKean leaned forward with his expression settling back into its dispassionate, calculating mode. “It all depends,” he said. “If the vaccine-to-brain cross-reaction is weak, perhaps few or none at all. But if the cross-reaction is strong, then conceivably every person who gets a dose might come down with the mania.”
“But I just got confirmation this morning from the CDC that over a million doses are in the works at ImCo and Virogen!”
“I urge you to use every means at your disposal to stop the vaccine before it’s too late. Insist they recall the product and shift to a G2-only vaccine. I’m sure G2 will provide a sufficient immunization. And I’ve just confirmed what I feared all along - that going ahead when G1’s
structure was unknown was foolish.”
“How will I ever convince them in time? There are dozens of new cases at Olympic Medical Center this morning, including some of the staff. We need a vaccine desperately. There’s no time to start over.”
“Nevertheless, a mass immunization with G1 could create a plague of madness much greater than the one you’re trying to stop.”
Erwin put a hand to her chest. She looked as panicky as I felt. “I’ll fight whatever battles I can,” she said. “But things have gone too far down the wrong path.”
“Thanks to unscientific fools like Holloman and his lapdog, Curman,” McKean muttered bitterly.
“I’d better get on the phone to Atlanta,” said Erwin. “And ImCo, and Virogen.”
After hasty goodbyes, McKean switched off the video connection. He turned to me with a morose look on his long face. “When science takes a back seat to politics and money, any horror is possible.”
“Is there nothing you can do?”
He shrugged. “I’m banished from my own laboratory. What can I do except watch from the sidelines? What about you, Fin? You still have your ways and means. Why don’t you publish an article against the Holloman vaccine online or in the local media? Admittedly, at this eleventh hour, it might be nothing more than Washington State’s epitaph.”
A deep chill ran through me. “That’s exactly what Gordon Steel said - that I would chronicle the end of our society!”
* * * * * * * * * *
Driving home, my way led past ImCo on Western Avenue. The sound of voices massed in protest caused me to pull into a load-zone parking spot and then walk to the front of ImCo. I was dismayed to see the number of pro-vaccine demonstrators had grown to several hundred.
“Vaccine now! Vaccine now!” they chanted.
“You’ve got to stop!” I shouted against the roar of their chant without much effect. “The vaccine is more dangerous than the virus!”
The crowd chanted on and only the few people nearest me even noticed. They gave me irritated glances that suggested my opposition was not welcome. Desperate to cause a greater reaction, I went after several of the signs people were carrying. I knocked one that read, “Vaccinate The People Now!” out of the hands of its carrier and went after another that read, “Vaccinate Workers, Not Execs.” When that sign was on the pavement I went after a third. But the next man was prepared for me. He drew his sign back like a baseball bat. Just as I noticed the sign’s post was made from a heavy closet dowel, he swung it hard at my head. I raised an arm to parry but the deflected post struck my forehead anyway. I went down. When I came to my senses I was sprawled on the pavement between the crowd and ImCo. The crowd continued chanting, “Vaccine now!” disdaining to help me. Slowly, groggily, I got to my knees. Then I rose unsteadily to my feet. I daubed my fingertips in a red trickle that flowed from my forehead.
The chanting paused, and someone shouted up at ImCo’s windows, “Vaccine for everyone! Not just the executive elite!”
“You got yours, Holloman,” cried another. “When do we get ours?”
A young man in a black T shirt with a red anarchist A printed on the front cried, “No more government control! Release the vaccine now!”
A bearded and disheveled man wearing a cardboard sandwich sign jostled against me. His board was covered in marking-pen drawings of crosses, crescent moons, and other religious symbols surrounding a central script: SAVE OUR SOULS FROM GOD’S WRATH! He shouted, “And He shall smite your mightiest warriors, and your smallest babes, and who shall be safe from the hand of God?”
A hysterical, weeping woman shouted at ImCo, “Why won’t you help us?”
A thin black man hollered, “Is the vaccine for whites only?”
A young white man beside him, wearing a pink ribbon on his lapel cried, “Homophobes!”
Another black-clad anarchist shouted, “The government made the virus to kill us all!”
As they resumed their chant, I glanced above the crowd. Behind them, lining the roof of a two-story power plant building, was a gathering of - “Crows!” I shouted, pointing over the crowd’s heads. More crows were flying in from the west to join a large aggregation already present. They were watching the crowd with great interest. “Look at all the crows, people!”
Some protestors turned their heads, but then shot me irritated looks because the significance of my concern was lost on them. The bulk of the crowd continued their chant, unaware.
Still feeling woozy from the blow to my head, I decided I had had enough. I walked back toward my car, but noticed the dark form of a large bird lying on the sidewalk. It flopped spasmodically, and the sight of it froze me in my tracks. It was a raven! Horrified, I watched it convulse in the throes of a fatal disease, the nature of which I had little doubt. I gaped at it for a moment, shaken by the notion that it must have flown across Puget Sound with the disease in its body, perhaps along with the crows now sitting on the building or flying over the crowd. Here was Gordon Steel’s death on the wing!
The raven stopped moving. As it settled flat on the concrete in death, I called Seattle Public Health Hospital and asked to speak with Kay Erwin. I explained about the raven and she replied, “By all means, bring it here. I’ll have someone waiting at the emergency entrance with a sterile containment box. You just be careful not to touch it yourself.”
I clicked off the phone and went to a newspaper stand, where I bought a singles newspaper and used it to carefully pick up and wrap the animal, which I put into the trunk of my car. I drove to the hospital where a staffer with a sterile mask and purple gloves waited at the curb. I got out and opened my trunk and the man took the raven, newspaper and all, and put it into a white box with biohazard symbols on its sides. He hurried back into the hospital and I drove home.
Chapter 20
At home, I checked the welt on my forehead in the bathroom mirror. It had quit bleeding but had swollen to an impressive size and was giving me a headache. I daubed away dried blood with a washcloth, took some ibuprofen and went to bed early after eating a few bites of dinner. I slept poorly, tossing and turning for hours, dreadfully afraid of the pestilence that seemed at hand. I mulled over every incident a hundred times and wondered what McKean was doing. Was he awake like me, a thousand thoughts crowding his mind?
I got up early the next morning wondering if society were still functioning. I logged into my Seattle Post Intelligencer account on my iPhone and read it over coffee. Under the headline A MODERN PLAGUE, several articles described widespread outbreaks of the disease on the north shore of the Olympic Peninsula, as well as a new massive outbreak that had breached the quarantine lines south of Neah Bay and sent maniacs raging into the streets of Forks. Another article described the deployment of 10,000 National Guard troops on the peninsula wearing full biowarfare suits and carrying M-16s. A third article covered the Holloman vaccine with an estimate of only two more days before it would be administered to the public.
The article gave little indication whether larger American society was aware how imminent its collapse might be. Not until I read a fourth article did I find any mention of Peyton McKean. A brief report on his firing ran in a narrow column below a page-wide banner advertising ladies’ undergarments. Below the ad’s bold declaration, WOMEN’S BRAZIERS HALF-OFF, McKean’s outburst at the press conference and his termination from ImCo were ascribed by Holloman to his “obsession with petty worries about the vaccine.” A quote from Curman described McKean as “egotistical and deranged.” So much for the man I considered society’s only real hope.
I decided to do what Gordon Steel had suggested. I would spend my day writing down the epitaph of our times. I left home at about 10:00 am and walked past ImCo, seeing no sign of the demonstrators or the crows. In the Pioneer Square district, I stopped at Cafe Perugia, hoping a triple shot would inspire some thoughts worth writing about a doomed society. Before going upstairs, I sidetracked to watch a scene developing at the Ortman Gallery. Two police cars were stopped with their
lights flashing. Glass was scattered on the sidewalk. I noticed with surprise that the harpoon was missing from its place in the broken window. A man inside was talking with two policemen and pantomiming the actions of a person who had smashed the window, snatched the harpoon, and run off down the alley.
Another surprise awaited me at my office building. The front door was ajar. I went in just as two police officers on foot rounded the corner, checking building fronts. Acting on a hunch, I went upstairs two steps at a time. As I reached the fifth floor, two things happened simultaneously. I saw that my office door had been jimmied, and one of the officers called from the first floor landing, “Hello, sir? We’d like to speak with you.”
The green enameled wooden frame of the door was split. It appeared to have been shouldered open. I guessed that this breakin was tied to the theft at the Ortman Gallery and knew the intruder’s identity when I saw his two-headed serpent sculpture sitting on my desk. As the officers’ foot scuffs started up the stairs, the lead cop called, “Police Officers, looking for a fugitive.” I stepped inside and a movement in a corner caught my eye. John Steel crouched there, peeking over the top of a five-drawer filing cabinet, holding the harpoon in one hand. He pressed a finger to his lips and tented his eyebrows imploringly.
The officer called again from the third floor landing, “Hello. Sir. Are you up there?” Only seconds remained before John Steel would be caught. I waved John down and he sank behind the cabinet again. As the first officer reached the top of the staircase and crossed the landing, I stepped into my open doorway, blocking his entry.
“Have you seen a tall Indian guy around here?” he asked.
“No.”
“Heard anything?”
“I just got here.”
He glanced around me to the right and left. Then he ran a hand along the split doorframe. “What’s this?”
“I…lost my key. I got mad and broke it a couple days ago.”