The Initials Project: JR-CSF and JR-FL

29 October 2013 by Nathalia Holt, posted in The Initials Project

For two years I worked with a strain of HIV called JR-CSF. Although I was well versed in how the virus behaved in human cells grown in a flask, I had no idea where the strain came from or how it received its name. The initials project was inspired by the work of Rebecca Skloot and her investigation of Henrietta Lacks, known in the lab only as HeLa. In this series we’ll explore the people and science that made the cells, viruses and reagents behind the initials and acronyms used everyday in labs worldwide. First up is the story of J.R.


Yoshio Koyanagi wrote the initials on the side of the vial in tiny print: JR-CSF. It was the first year of his postdoctoral training and, in his own words; he “didn’t know the rules of nomenclature.” Instead he named the virus based on where it came from.  The name was simple and descriptive. He took the samples from a man whose initials were J.R. Then he added which part of the body they were isolated from. JR-CSF came from the filtered liquid of J.R.’s cerebrospinal fluid. JR-FL, on the other hand, was isolated from the frontal lobe of J.R.’s brain.

This was the first HIV positive patient Yoshio had ever isolated virus from. The year was 1986. On a warm evening in June, J.R. passed away. His disease was rapid. He had AIDS encephalopathy, a horrible disorder where the virus shuts down the brain. In his last days the virus left him with a crippling dementia. As if that wasn't enough, J.R. also suffered from a cancer commonly found in those with HIV called Kaposi’s sarcoma. It left red lesions across his body and made it difficult for him to breathe. He wasn’t alone in his illness. His partner had recently succumbed to the same unexplainably rapid AIDS disease.


It was the early days of the epidemic. Two years earlier, in 1984, HIV had been identified as the cause of AIDS. Despite this knowledge, there was no treatment available. Doctors could offer little but supportive care. In 1987 the FDA approved AZT, the first drug effective against HIV. It was a year too late for J.R.


Yoshio went to graduate school at Kyoto University in Japan before coming to Irvin Chen’s lab at UCLA for his postdoc. He entered the autopsy room on June 11, 1986. Yoshio was interested in HIV and the central nervous system. When he took the virus from J.R.’s brain and spinal fluid he couldn’t know that the samples he was extracting would become critically important to HIV research.


What makes J.R.’s samples so special is that even though they were both extracted from the central nervous system, one from the brain and one from the cerebrospinal fluid, they are genetically distinct. Although they came from the same person, they are two viruses. They even infect different cells. The virus originating from the brain can infect macrophages, an immune cell that protects us by eating up things like bacteria and dead cells. The description of J.R.’s viruses, published in 1987, was an early glimpse inside HIV’s diverse and pathogenic world. But the real gift J.R. gave us is the unique ability of his viruses to behave as aggressively in a lab dish as they once did in his body. The pathogenic nature of his viruses is partly determined by the HIV strain itself but also selected from the pressure a person’s immune system places on the virus. Make no mistake; J.R.’s viruses are valuable because he made them that way.


In the 25 years since J.R.’s viruses were isolated, they have been grown in hundreds of laboratories all over the world. The virus has become a respected lab-adapted strain that can be counted on to kill human cells and cell lines in culture, producing large quantities of itself in the process. The strain has been used in countless studies: from vaccine development to microbicides to eradication research. There’s hardly an area of HIV research that J.R. hasn’t had some role in.


Today thousands of HIV researchers around the world work with JR-CSF and JR-FL on a daily basis without any thought of the person behind the initials. HIV and J.R. are both literally and figuratively intertwined. Even after billions of rounds of replication, the genomes of JR-CSF and JR-FL hold the imprint of the person who carried them. Part of J.R. is forever wrapped up in the replicating virus. Similarly, the initials J.R. have become part of HIV’s identity, indistinguishable from the virus for those familiar with the samples. Every day students and postdocs thaw tiny vials with the labels JR-CSF and JR-FL neatly printed on opaque labels. They grow the virus in a warm incubator, writing J.R. on the side of flasks, tubes, plates. They print J.R. in their lab notebooks and then type his initials again in their research papers. His initials are spoken aloud in meetings, presentations, and the hushed tones that herald new data. He is everywhere and yet nowhere. Thank you J.R.


Interested in working with J.R.’s samples? You can order them from the NIH repository here

Yoshio Koyanagi, MD/PhD is a professor at Kyoto University and still works with JR-CSF and JR-FL you can find his lab here

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