Full-Length Characterization of Hepatitis C Virus Subtype 3a Reveals Novel Hypervariable Regions under Positive Selection during Acute Infection

Humphreys I, Fleming V, Fabris P, Parker J, Schulenberg B, Brown A, Demetriou C, Gaudieri S, Pfafferott K, Lucas M, Collier J, Huang KH, Pybus OG, Klenerman P, Barnes E.

J Virol. 2009 Nov;83(22):11456-66. Epub 2009 Sep 9.

Hepatitis C virus subtype 3a is a highly prevalent and globally distributed strain that is often associated with infection via injection drug use. This subtype exhibits particular phenotypic characteristics. In spite of this, detailed genetic analysis of this subtype has rarely been performed. We performed full-length viral sequence analysis in 18 patients with chronic HCV subtype 3a infection and assessed genomic viral variability in comparison to other HCV subtypes. Two novel regions of intragenotypic hypervariability within the envelope protein E2, of HCV genotype 3a, were identified. We named these regions HVR495 and HVR575. They consisted of flanking conserved hydrophobic amino acids and central variable residues. A 5-amino-acid insertion found only in genotype 3a and a putative glycosylation site is contained within HVR575. Evolutionary analysis of E2 showed that positively selected sites within genotype 3a infection were largely restricted to HVR1, HVR495, and HVR575. Further analysis of clonal viral populations within single hosts showed that viral variation within HVR495 and HVR575 were subject to intrahost positive selecting forces. Longitudinal analysis of four patients with acute HCV subtype 3a infection sampled at multiple time points showed that positively selected mutations within HVR495 and HVR575 arose early during primary infection. HVR495 and HVR575 were not present in HCV subtypes 1a, 1b, 2a, or 6a. Some variability that was not subject to positive selection was present in subtype 4a HVR575. Further defining the functional significance of these regions may have important implications for genotype 3a E2 virus-receptor interactions and for vaccine studies that aim to induce cross-reactive anti-E2 antibodies.

So, about my favourite song…

Let me tell you about my favourite song.

There’s a song link and lyrics coming up, but first let’s have a bit of a yarn…

‘Leopard Limousines’ is on Joe Strummer’s first solo effort, a record I stumbled upon in the uni radio station catalogue as I thumbed drunkenly through looking for Clash vinyl the night he died. Looking for Joe Strummer, punk rock warlord, I found John Graham Mellor – and struck gold.

It remains the only record I’ve ever stolen from a station, and the only one I want played at my funeral. As possibly the most underrated and hardest-to-find commercial recording of Joe’s (only on vinyl, and those are like hens’ teeth) you might not know it very well, so here’s a quick intro:

It’s the arse-end of the Eighties (yes, they WERE shit), The Clash are a distant memory, and Joe Strummer’s been kicking his heels, jobbing in films and battling the black dog in Spain for a few years while an indifferent public obliviously buy Timmy Mallet’s ‘Bombalerina’ by the thousand and the Tories continue to fuck up the country.

Encouraged by a chance encounter, and with a back-breaking load of frustration, regret and wanderlust, Joe holes up in LA with a few cronies to have another crack at making music, his first named recordings for over 4 years…

‘Earthquake Weather’ (Sony, 1989) turns out to be more rambling and unfocused than any of his previous work; in particular (drawing on his penchants for soundtrack and Western imagery) the lyrics are cinematic where the Clash were hyperactive; the message ambiguous where they were bellicose.

The unsettling mixture of organic sounds, raw emotion and diffuse themes failed to chime with the concerns of either his core punk fans (by now many of them, in any case, downing mohawks and getting on with the business of family life) or music nerds more interested in Detroit or Manchester than Andalucia via California. The record performed poorly in the shops; aside from a spell with The Pogues, Joe wouldn’t make music again for another half-decade.

Today the album plays more like a sketch-pad than a fully-finished work, with bold, yet unfinished ideas (‘Sikorsky Parts’); standard Joe Strummer stompalongs (‘Gangsterville’ in particular recalling the worst moments of Cut The Crap) or ragga covers (‘Ride Your Donkey’) and the odd gem (‘Island Hopping’, ‘Sleepwalk’). This last set of songs are most at odds with Joe’s public image as the air-punching, rabble-rousing ‘punk rock warlord’ – but in these plaintive, hesitant vocals (“… what good would it be / If you could change every heartache that ran through yout life and mine,” he mourns, on ‘Sleepwalk’) I think we get a much more interesting glimpse into his life and motivations than on all 6 sides of ‘Clash on Broadway’.

‘Leopardskin Limousines’ is the best example of this, and is worth a listen in that sense alone – but the off-kilter piano ostinato, restrained guitar and gravelly vocals elevate it, for me, from ‘best Strummer tune’ to My Favourite Song status.

The lyrics read like an atheist’s prayer book, or perhaps a letter of atonement to his family. Remorse and despair are mixed with glimmers of wry hope and fond reminiscence, and it’s this last emotion floors me; where Joe Strummer conjures up “…Charlie Parker, Chevys / And late night barroom brawls” we stand beside him and see all that, as he intended. But now, after his passing, we can simultaneously peer round the kitchen door at John Mellor, up alone with his demons in the small hours of the night, slumped against the fridge slugging brandy and trying to forget.

Each time I listen, this song throws up more and more questions: would the record do better these days, carefully filtered through the networks of bloggers, rather than foisted on an unreceptive mass market by Sony? Would the songs be more fully realised, given modern tools like GarageBand and ProTools to play with? Why was it so long before he recorded again? And – crucially – who was he writing to? His wives, kids, mistresses, father – or himself?

But the question I always come back to, as I did the first time I heard it, sitting devastated on the radio station floor that December, is ‘why did he have to go?’

Joe Strummer R.I.P.

Listen to it here:
http://www.youtube.com/watch?..v=o7bF63VeTiY

Leopardskin Limousines (J Strummer)

Noontime the lunchstand tilts
It’s you baby walking in with your stilts
You don’t have to eat here no more
Cos the sauerkraut’s been on the dog-bowl floor
They made an old film of this
It shows in Hindu out on Air Pacif
Shoulda seen it coming ’bout a mile away
Especially when you don’t hear no harmonica play

What you can see is something you saw
When you were a little girl
Some picture passed by the Hayes Commission
About a prairie and a Kansas whirl
It’s true I didn’t have a part in it
I was working out at Disneyworld
Dressing like a duck, not giving a fuck
Baby you can dream it’s a pearl

People gonna wanna Xerox you baby
It’s a good thing you ain’t a Chickasaw
Or your soul would take the overnight train
To Pittsburgh calling Baltimore
People gonna wanna Xerox you baby
What will it do to your mind?
Hang gliding off the Grand Canyon
In a Coney Island for the blind

With me, it’d be Charlie Parker, Chevys
And late night barroom brawls
With real or imgainary friends and enemies
Who strike their heads when they fall
On the chassis of a classic Bull Nose special
That adorned our livingroom wall
Nobody’d be disappointed, if you’re the one they wanted
Blazing out across the waterfall

People gonna wanna Xerox you baby
They got a quota to fill
Got some cat named Juliean
And a Jap in a pad on the top of the hill
People gonna wanna Xerox you baby
It’s a good thing you ain’t a Chickasaw
Or your soul would take the overnight train
To Pittsburgh calling Baltimore

Suppose I should drag my stuff on out
But I don’t like the memories
Found a pint of brandy on top of the fridge
And it’s working like an antifreeze
So California is running short of water, oh
The magazine turns in the breeze
It’s the bargain of a lifetime dreaming of gold
Baby look in the trees

It’s your Chinese year of the animal
And it must be one that preens
Those firecrackers going down the hill
Signify the end of our dreams

It’s gonna be so beautiful
In those Leopardskin Limousines
When they spread you out in white
All over Harpers and Queens.