Researchers map 209 flu virus genomes

first_imgOct 6, 2005 (CIDRAP News) – Influenza researchers marked a milestone yesterday by publishing a report on the complete genetic mapping of 209 samples of human flu viruses, vastly increasing the supply of genetic data on flu. The report, published in Nature, is one of the first fruits of the Influenza Genome Sequencing Project, which aims to trace the genetic blueprints of thousands of flu viruses. The project, announced in November 2004, is a joint effort of the National Institute of Allergy and Infectious Diseases (NIAID), the National Center for Biotechnology Information, the Wadsworth Center of the New York State Department of Health in Albany, and The Institute for Genomic Research (TIGR) in Rockville, Md. The flu genome sequencing project is now being expanded to include avian flu, in an effort to learn how often avian strains cross into humans, the article says. The H5N1 avian strain now circulating in Asia has already infected more than 115 humans. Experts fear it could soon gain the ability to spread readily from person to person, thereby launching a pandemic. “These new data give us the most comprehensive picture to date of how influenza viruses evolve and are transmitted throughout human populations,” NIAID Director Anthony Fauci, MD, said in a news release. He said the new information could lead to better vaccines, drugs, and diagnostic tools for flu. “As a result of this project, the number of complete human H3N2 influenza virus genomes in GenBank [a public online database] has already grown from just seven genomes to over 200,” the article says. The samples analyzed include 207 H3N2 viruses and two H1N2 isolates, which were gathered in New York state over five flu seasons, from 1998-99 through 2003-04. “The sequenced strains were not preselected because of their virulence or unusual characteristics, giving researchers an unbiased view of flu virus evolution as it moved through a varied human population,” the NIAID statement said. See also: They detected a number of mutations (changes in particular amino acids) that occurred during the study period, and also found three cases in which strains traded whole gene segments (reassortments). In July some members of the team reported in detail on the most significant of these events, in which two groups, or clades, of H3N2 viruses acquired the hemagglutinin gene from a third H3N2 group. That gave rise to the Fujian strain of flu, which predominated in the 2003-04 flu season. The vaccine that year was not well matched to the Fujian strain and had reduced effectiveness. The viruses were surprisingly varied. “Even within a geographically constrained set of isolates, we have found surprising genetic diversity, indicating that the reservoir of influenza A strains in the human population—and the concomitant potential for segment exchange between strains—may be greater than was previously suspected,” the researchers write. By carefully cataloging mutations and reassortments, “we can begin to get the first real picture of the rate of mutational events underlying influenza A virus evolution,” the researchers write. The research was done by a large team, with Elodie Ghedin of TIGR listed as the first author. They published their report the same day other teams reported on the re-creation of the deadly 1918 pandemic flu virus and a finding that the 1918 virus closely resembled avian flu viruses. Ghedin E, Sengamalay NA, Shumway M, et al. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 2005 Oct 5 (advance online publication) [Full text] Ghedin and colleagues say that until now, scientists had fully mapped and published the genomes of only a few strains of human flu viruses. Most of the published data pertain to short fragments of the genes for the virus’s two key surface proteins, hemagglutinin and neuraminidase. Jul 26, 2005, CIDRAP News story “Flu viruses can evolve in unsuspected ways, study says”last_img read more

Once again, Angels can’t find a way to beat sizzling Indians

first_imgBesides that, the Angels cracked the door for the Indians by failing to come up with a catchable fly ball, and they let them off the hook by being unable to convert their scoring opportunities.The result was seeing their losing streak stretch to four games, their longest skid since April.At 76-76, the Angels are 2½ games behind the Minnesota Twins in the American League wild-card race after the Twins routed the Tigers, 12-1, Thursday night in Detroit. The Angels have 10 games left.Perhaps the best news for the Angels is that next week the Twins play the Indians three times. Minnesota’s six other games are with the Tigers (62-91).“They’re a terrific club,” Manager Mike Scioscia said of the Indians. “It’s pretty evident that if we do the things we’re good at on the field, we’re going to set up games to give ourselves a chance to win. We didn’t do enough this series.” Related Articles Angels Notes: Andrew Heaney feeling good about progress, but time running short Scioscia always talks about “getting the game on our terms,” which means getting an early lead and holding it. The Angels had not had a single lead in any of their first five games against the Indians. An Albert Pujols RBI single in the first temporarily ended that streak, but then Encarnacion hit a hanging curveball out in the second to tie it. Angels at Astros: Friday game time, TV channel, starting pitchers center_img The game was then decided in the fifth, when the Angels cracked the door. Bridwell got Yan Gomes to hit a lazy fly ball into right center to lead off the inning. Mike Trout, Kole Calhoun and second baseman Brandon Phillips all converged on it, and the ball hit Calhoun’s glove and dropped, for a single.Trout said he lost it in the sun, and Calhoun had a long run to try to make up the ground to catch it.Giovanny Urshela then hit a line drive toward left. Andrelton Simmons leaped and got a glove on the ball, but he couldn’t bring it down.The Indians still had runners at first and second, after a failed sacrifice, when Lindor belted a three-run homer to straightaway center, his second tie-breaking homer in as many games.The Angels couldn’t overcome what Lindor produced on one swing, as they were held down by a collection of Indians relievers.The Indians started Danny Salazar, a starter who lost his job, in order to give the top five starters an extra day of rest. Their best hope was in the seventh, when they managed a surprising rally against left-hander Andrew Miller, one of the Indians’ dominating relievers. Calhoun and Luis Valbuena, ironically a pair of lefties, both drew walks against Miller, sandwiched around Simmons’ infield hit.With the bases loaded and one out, Miller came back and struck out both C.J. Cron and Martin Maldonado, needing the minimum six pitches.After that, the Angels managed only a Trout single in the final two innings, before packing up for Houston and the final stretch of crucial games.“We obviously want to be ahead of (the Twins), but we’re still in it,” Trout said. “We’ve got to keep pushing and try to win games.” PreviousCleveland Indians catcher Yan Gomes, left, celebrates with relief pitcher Tyler Olson after their win against the Los Angeles Angels during a baseball game in Anaheim, Calif., Thursday, Sept. 21, 2017. (AP Photo/Chris Carlson)Angels shortstop Andrelton Simmons stops a grounder by Cleveland’s Edwin Encarnacion during the sixth inning of Thursday’s game at Angel Stadium. Simmons was able to throw him out at first, but the Angels lost, 4-1, and were swept by the hottest team in baseball. (Photo by Paul Rodriguez, Orange County Register/SCNG)The Angels’ Brandon Phillips, left, tries to avoid the tag by Cleveland shortstop Francisco Lindor as he tries to stretch a single into a double during the first inning of Thursday’s game at Angel Stadium. (Photo by Paul Rodriguez, Orange County Register/SCNG) SoundThe gallery will resume insecondsAngels third baseman Luis Valbuena makes the force out on Cleveland catcher Yan Gomes in the fifth inning in Anaheim on Thursday, September 21, 2017. (Photo by Paul Rodriguez, Orange County Register/SCNG)Angels starting pitcher Parker Bridwell tries to compose himself after giving up a home run to Cleveland’s Edwin Encarnacion in the second inning in Anaheim on Thursday, September 21, 2017. (Photo by Paul Rodriguez, Orange County Register/SCNG)Cleveland Indians’ Edwin Encarnacion, right, rounds the bases after a home run off Angels starting pitcher Parker Bridwell during the second inning of a game in Anaheim, Calif., Thursday, Sept. 21, 2017. (AP Photo/Chris Carlson)Angels shortstop Andrelton Simmons, right, tries to dig out a throw in the dirt as he tries to pick off Cleveland catcher Yan Gomes in Anaheim on Thursday, September 21, 2017. (Photo by Paul Rodriguez, Orange County Register/SCNG)Angels catcher Martin Maldonado makes the catch on a foul ball by Cleveland’s Edwin Encarnacion behind the plate in Anaheim on Thursday, September 21, 2017. (Photo by Paul Rodriguez, Orange County Register/SCNG)Cleveland Indians’ Edwin Encarnacion watches his home run against the Angels during the second inning of a game in Anaheim, Calif., Thursday, Sept. 21, 2017. (AP Photo/Chris Carlson)Cleveland Indians first baseman Carlos Santana fields a ball hit down the first base line by the Angels’ Kole Calhoun during the fourth inning of a game in Anaheim, Calif., Thursday, Sept. 21, 2017. Calhoun was out at first. (AP Photo/Chris Carlson)The Angels’ Albert Pujols watches his RBI-double against the Cleveland Indians during the first inning of a game in Anaheim, Calif., Thursday, Sept. 21, 2017. (AP Photo/Chris Carlson)Cleveland Indians’ Francisco Lindor celebrates past Angels catcher Martin Maldonado after his three-run home run during the fifth inning of a game in Anaheim, Calif., Thursday, Sept. 21, 2017. (AP Photo/Chris Carlson)The Angels’ Mike Trout celebrates in the dugout after scoring on a double by Albert Pujols during the first inning of a game against the Cleveland Indians in Anaheim, Calif., Thursday, Sept. 21, 2017. (AP Photo/Chris Carlson)The Angels’ Justin Upton slams his bat into the ground and breaks it after flying out against the Cleveland Indians during the third inning of a game in Anaheim, Calif., Thursday, Sept. 21, 2017. (AP Photo/Chris Carlson)Cleveland’s Francisco Lindor, second from left, gets a high five from teammate Erik Gonzalez as he crosses home plate after hitting a three-run home run off of Angels starting pitcher Parker Bridwell in Anaheim on Thursday, September 21, 2017. (Photo by Paul Rodriguez, Orange County Register/SCNG)A pick off attempt on Cleveland’s Abraham Almonte, right, gets by Angels first baseman C.J. Cron, left, in Anaheim on Thursday, September 21, 2017. Almonte took second on the play. (Photo by Paul Rodriguez, Orange County Register/SCNG)Los Angeles Angels manager Mike Scioscia watches during the sixth inning of a baseball game against the Cleveland Indians in Anaheim, Calif., Thursday, Sept. 21, 2017. (AP Photo/Chris Carlson)Los Angeles Angels’ Albert Pujols reacts after flying out against the Cleveland Indians during the eighth inning of a baseball game in Anaheim, Calif., Thursday, Sept. 21, 2017. (AP Photo/Chris Carlson)Angels shortstop Andrelton Simmons dives to his left to field a sharp grounder up the middle by Cleveland’s Yan Gomes in the ninth inning in Anaheim on Thursday, September 21, 2017. Simmons was able to throw him out at first. (Photo by Paul Rodriguez, Orange County Register/SCNG)Angels third baseman Luis Valbuena turns as he tries to throw out the runner in the sixth inning against Cleveland in Anaheim on Thursday, September 21, 2017. (Photo by Paul Rodriguez, Orange County Register/SCNG)Angels starting pitcher Parker Bridwell delivers a pitch against Cleveland in the first inning in Anaheim on Thursday, September 21, 2017. (Photo by Paul Rodriguez, Orange County Register/SCNG)Angels manager Mike Scioscia, center, argues a call by the plate umpire against Cleveland in Anaheim on Thursday, September 21, 2017. (Photo by Paul Rodriguez, Orange County Register/SCNG)Manager Mike Scioscia, left, and slugger Albert Pujols, second from right, are among those watching from the dugout as the Angels bat in the ninth inning of their 4-1 loss to the Cleveland Indians on Thursday afternoon at Angel Stadium. (Photo by Paul Rodriguez, Orange County Register/SCNG)Cleveland Indians catcher Yan Gomes, left, celebrates with relief pitcher Tyler Olson after their win against the Los Angeles Angels during a baseball game in Anaheim, Calif., Thursday, Sept. 21, 2017. (AP Photo/Chris Carlson)Angels shortstop Andrelton Simmons stops a grounder by Cleveland’s Edwin Encarnacion during the sixth inning of Thursday’s game at Angel Stadium. Simmons was able to throw him out at first, but the Angels lost, 4-1, and were swept by the hottest team in baseball. (Photo by Paul Rodriguez, Orange County Register/SCNG)NextShow Caption1 of 23Angels shortstop Andrelton Simmons stops a grounder by Cleveland’s Edwin Encarnacion during the sixth inning of Thursday’s game at Angel Stadium. Simmons was able to throw him out at first, but the Angels lost, 4-1, and were swept by the hottest team in baseball. (Photo by Paul Rodriguez, Orange County Register/SCNG)ExpandANAHEIM — This time of year, with the games meaning this much, the Angels couldn’t simply shrug their shoulders and accept that they ran into a historically hot team.After the Cleveland Indians beat the Angels, 4-1, on Thursday, completing a three-game sweep and winning for the 27th time in 28 games, the Angels were still shaking their heads, thinking they could have won.“We made mistakes,” Parker Bridwell said. “They didn’t completely beat us, you know what I mean? We did get swept, but we made mistakes that hurt us, and by mistakes I’m talking pitches.”Bridwell gave up all four runs on two homers, misplaced pitches to Edwin Encarnacion in the second and to Francisco Lindor for a three-run, tie-breaking homer in the fifth. Newsroom GuidelinesNews TipsContact UsReport an Errorlast_img read more