virology blog

About viruses and viral disease

Papers

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When journal articles began to appear online in pdf form, I started to collect them on my computer’s hard drive. In theory the pdfs can be accessed very quickly, as opposed to finding a printed article in a filing cabinet. To help find papers more quickly, I devised a filing system with nested folders. Unfortunately, as the file structure became deeper and deeper, it was more and more difficult to find papers: drilling down many folder levels just isn’t efficient. When Spotlight came to the Macintosh, it didn’t help; Spotlight is slow and returns too many hits. In the past years I’ve resorted to printing out copies of important papers, and storing them in strategically placed piles. But this isn’t the way the digital age should work!

I’ve been looking for a solution to the pdf conundrum. I tried Yojimbo, a nice program by Bare Bones Software, the makers of BBEdit (which I use to post to this blog), but it wasn’t designed for the scientific literature. Then this week I stumbled across Papers – written by Alexander Griekspoor (Mek) and Tom Groothuis (Tosj) of mekentosj.com (yes, it’s a play on ‘Macintosh’). These are two fellows who, as Ph.D. students, wrote a number of Mac programs for use in the laboratory. My favorite is EnzymeX, but there are other useful programs as well. These programs leverage the technologies available in OS X, together with visually useful interfaces, to provide solutions to laboratory problems.

Papers is a program for obtaining and organizing scientific articles. I discovered it yesterday, downloaded it today, and after five minutes of using it I’m sold. If you have an existing pdf collection, you can add it to Papers, assign keywords, and organize the paper into categories. The pdfs can be read directly in Papers. You can also search PubMed from within the program, download pdfs, and have them placed into Papers automatically. This description doesn’t even begin to scratch the surface of what Papers can do. I’m sure it will become an important part of my article workflow. If it doesn’t, I’ll let you know.

One problem with pdfs not addressed by Papers is portability. It’s great to have Papers store all my pdfs on my work computer, but what if I want to work on them elsewhere? I could put them on a portable drive, but I don’t want to worry about carrying it around. Better would be to have the pdfs stored online. Yojimbo allows collections to be stored on .Mac – but you have to subscribe to that service from Apple. I’d rather be able to store pdf archives on any WEBDAV server, like those you can store your iCal calendars on. I’m going to suggest to Mek and Tosj to build this ability into future versions of Papers.

Bio Job Blog

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If you are thinking about a career in science, you should visit Bio Job Blog. The blog is written by Cliff Mintz of Bioinsights, Inc., a company that offers services related to bioscience and biotech careers, pharmaceutical and science jobs. Bio Job Blog is informative, sometimes amusing, and thought-provoking.

Cliff Mintz is a very old friend of mine. We were both undergraduates at Cornell University in the early 1970s; after graduation we lost track of each other. I didn’t see Cliff until the early 1980s, when he showed up at Columbia to do a postdoctoral fellowship with my colleague, Howard Shuman. We now live near each other and meet at the Jersey shore at least once a year to talk about – what else? – science.

HubMed

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Virologists rely on the research literature not only to publish their findings, but to keep up with what other virologists are doing. PubMed, a database that provides citations from many life sciences journals and related resources, provides an easy way to search the entire biomedical literature and is used by most virologists on a daily basis.

HubMed is an alternative to the PubMed interface. Special features (taken from the HubMed website) include date- or relevance-ranked search results; web feeds for regular updates of published literature matching any search; clustering and graphical display of related articles; expansion of query terms; direct export of citation metadata in many formats; linking of keywords to external sources of information; manual categorisation (tagging) and storage of interesting articles.

A related site is HubLog, a blog by the creator of HubMed which provides insight into using HubMed and general information-related hacking.

VHSV – A Deadly Virus of Fish

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vsv virionI came across an article in Saukvalley.com about VHSV, or viral hemorrhagic septicemia virus, which causes disease in fish. I have never worked on viruses of fish, but they’re fascinating, and economically very, very important. So let’s have a look at what this article is about.

VHSV causes a very serious disease of fresh and saltwater fish. Signs of VHSV infection include hemorrhaging, anemia, bulging eyes, and bloated abdomens, but not all fish display symptoms. The virus is lethal, causing outbreaks in which thousands of fish die.

VHSV is a member of the family Rhabdoviridae, which also includes the well known human pathogen rabies virus. However, VHSV is not known to infect humans. Members of the Rhabdovirus family have a enveloped capsid containing a single-stranded RNA genome of negative polarity. The diagram show a typical rhabdovirus, vesicular stomatitis virus.

VHSV was first isolated in the middle of the 20th century, when it became a disease of cultured rainbow trout. Since then the virus has been found to cause disease in many other fresh and saltwater fish. It first infected freshwater fish in the western hemisphere in 2005, when it was reported in Lake Ontario. The article in saukvalley.com cited above suggests that the virus might be headed for Lake Michigan, because it has been detected in a northern region of Lake Huron only 20 miles away. The article discusses the potential effect of the virus on the $4 billion per year sport fishing industry in the Great Lakes.

How does the virus spread? In the water, of course: infected fish excrete the virus in their urine. The virus probably made its way into the Great Lakes in the ballast of ships – the water stored in the bottom to stabilize the vessels.

Polio in Pakistan and Afghanistan

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Transmission of wild poliovirus continues in four countries: Afghanistan, India, Nigeria, and Pakistan. From January 2006 to February 2007, the number of polio cases increased in Pakistan and Afghanistan. Poliovirus continues to circulate in these countries because insufficent numbers of infants receive three doses of oral polio vaccine – 69% and 64% in Afghanistan and Pakistan, respectively. More importantly, coverage varies significantly within the countries, with higher rates in areas with good health infrastructure, easy access, and high literacy.

To eradicate poliovirus from these countries, it will be necessary to overcome a very large challenge: to access and vaccinate children along the large border between the two countries that is remote and insecure. This border area is the main virus reservoir in the region and, because of frequent border crossings, is a principal source of poliovirus spread into other areas.

This problem illustrates the sad reality that control of disease depends not only upon good science – developing an effective vaccine – but also social, cultural, and political issues well beyond the knowledge of most scientists. Immunization truly spans multiple disciplines.

For more information, see MMWR.

Eradication of Measles in South Korea

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MMWR reports on 6 April 2007 that measles has been eliminated from South Korea. The history of measles in South Korea provides a useful example of how immunization practices need to be flexible to achieve their goals.

Measles vaccine was first introduced into South Korea in 1965, and was included in the national immunization program in 1983 as part of the measles, mumps, and rubella vaccine. Two doses were given to children at 12-15 months and 4-6 years. Despite this approach, measles continued to occur, exemplified by an epidemic in 2000-2001 of 55,000 reported cases and seven deaths. Most of these infections occurred in children, indicating that vaccination was not sufficient and that circulation of measles virus continued.

In 2001, South Korea declared a goal of establishing measles by 2005, and developed key strategies, including requiring two doses of measles vaccine for school entry by 7 years of age; carrying out vaccination campaigns among children 8-16 years to cover those who were missed at an earlier age; and including laboratory confirmation of reported cases in the surveillance program.

These strategies have been very successful. Before the eradication plan, there were multiple measles epidemics in South Korea, with annual cases ranging from two to 32,647. As of November 2006, no cases of measles have occurred, and international authorities have concluded that measles has been eliminated from the country.

Measles virus still circulates in much of the world, and therfore immunization must be continued in South Korea if the disease is to be kept in check. If there is any relaxation of immunization – likely given that the infection is no longer a problem – the virus is likely to spread again.

WHO has declared that after polio is eradicated, they will turn their efforts to measles virus. While the outcome of measles immunization programs in South Korea will surely be used to promote the global effort, it will be much more difficult to eradicate the disease globally.