Uses of Phylogenetics

Uses of Phylogenetics

Evolutionary models: applications Examples from Clinical Virology Dr Gert van Zyl NHLS, Tygerberg and Stellenbosch University Case 1 Mystery illness causes paralysis in young Namibian adults [email protected]; on behalf

of; ProMED-mail [[email protected]]; 2 June 2006; 19:00 Panic is sweeping through suburbs north of Katutura (Windhoek) after 3 people died and 19 others were hospitalised with a disease that still has to be identified. A press release from the Ministry of Health and Social Services last night indicated that the disease was not confined to the Khomas Region, and that cases of "undiagnosed paralysis" among adults had

been reported in the Otjozondjupa and Hardap regions. A media briefing is scheduled for this morning to reveal information related to the outbreak. Well-placed hospital sources confirmed yesterday that 2 other people were fighting for their lives in the Intensive Care Unit (ICU) of the Windhoek Central Hospital after contracting the mystery disease. Another case of a strange disease in Namibia 39 year old man from Aranos

He complained of stomach pain, fever, weakness in his legs on 8 May 2006 He was admitted in Windhoek with leg weakness and had to be intubated for respiratory failure (could not breathe adequately). He was ventilated and subsequently died after more than a week in intensive care. Prior history: He was admitted from his farm in Aranos on 25 April for a cholecystectomy on 27 April, done in a

Windhoek private hospital. Stool specimen collected on the 15th of May was cultured for poliovirus wild type poliovirus was isolated Could this be Polio? Namibia had been poliovirus free since 1995 The only link between the mystery illness in Katutura and the Aranos case was the

mans prior visit to Windhoek Poliovirus is usually a disease of children, but almost all cases in Katutura were young adult males Experts are convinced it is not Polio Of the initial 34 cases with acute flaccid paralysis Age range between 5 and 76 years

13 of the 18 cases with age indicated (72%) were aged between 20 and 35 yrs Age: highly unusual for polio Concentration around Windhoek Unusually high death rate: 17/136 Experts said this is not Poliovirus the Aranos case is unrelated (they did not know of his short stay in Windhoek)

Next page: Map of prior poliovirus circulation WHO: WEEKLY EPIDEMIOLOGICAL RECORD, NO. 7,17 FEBRUARY 2006 The outbreak unfolds Poliovirus detected

Poliovirus-1 was isolated in 19 cases in Namibia All older than 14 years of age (14-59y) 79% were 15-19 years old 17/19 (89%) were male Explanation for this unusual outbreak

History of vaccination Migration Women care for children and may be indirectly vaccinated (children wearing nappies excrete vaccine virus) Phylogenetics of Poliovirus Where did this virus come from? There are three polioviruses: PV-1,2 and 3

An important structural gene, the VP1 gene (906 nucleotides) was sequenced Phylogenetic tree of PV-1 vaccine strain Nigerian strain Indian Strains

Angola Strains Indian Strain Angolan Strain Namibian Strains Findings from phylogenetic analysis All isolated viruses were PV-1 and were closely related Poliovirus molecular clock yields a 1% change per year Viruses had a 2.5% difference from parental Indian

strains indicating that the virus had been in Africa for at least 2.5 years The Namibia viruses matched closely with a strain isolated in Angola The viruses belonged to the South Asia Strain Polio virus 1 group (SOAS) originating from India Another poliovirus tree: SOAS introduced into Australia

Stewardson AJ, Roberts JA, Beckett CL, Prime HT, Loh P-S, Thorley BR, et al. Imported case of poliomyelitis, Melbourne, Australia, 2007. Emerg Infect Dis [serial on the Internet]. 2009 Jan [date cited]. Available from http://www.cdc.gov/EID/content/15/1/63.htm Role of phylogenetics in outbreaks How will phylogenetic trees compare? A viral strain that has recently been imported into a country

A viral strain that has been circulating for a long period How can one trace the source of the outbreak? Why is this important for outbreak control? References Barry D. Schoub, Expert Commentary Namibia Polio

Outbreak. Communicable Surveillance Bulletin: August 2006 Stewardson AJ, Roberts JA, Beckett CL, Prime HT, Loh P-S, Thorley BR, et al. Imported case of poliomyelitis, Melbourne, Australia, 2007. Emerg Infect Dis [serial on the Internet]. 2009 Jan [date cited]. Available from http://www.cdc.gov/EID/content/15/1/63.htm World Health Organisation. Weekly Epidemiological Record. 2006, 81, 425432

Gert van Zyl. The Namibian polio outbreak: reintroduction into fertile soil. SA Fam Pract 2006:48(7) Case-2 Largest hospital-related HIV outbreak ever recorded: Foreign health care workers, working in Libya accused of deliberately infecting their patients

Foreign doctors accused of deliberately infecting children in Al-Fateh Hospital (Benghazi, Libya) in 1998 Largest hospital acquired outbreak of HIV in history

The story World Organization, Libya investigates hospital acquired outbreak > 400 children infected with HIV Specimens sent for analysis in September 1998 6 Foreign HCWs: 5 Bulgarian Nurses and 1 Palestinian Doctor accused of deliberately infecting the children (these HCWs all arrived from March 1998 to August 1998)

Yerly et al. JID 2001;184 (1 August) Report in JID No epidemiological data except that the children were infected during 1998 were provided by WHO in Lybia Published in Science Magazine

Two of the worlds foremost HIV experts Vittorio Colizzi and Luc Montagnier investigated the outbreak: Colizzi and Montagnier were able to obtain blood samples and medical records from the children, examine the hospital, and interview its staff. It soon became apparent, says Colizzi, that this is a classic nosocomial infection in which tainted blood is accidentally passed between patients through poor hygiene practices, such as the reuse of disposable

syringes and catheters, insufficient sterilization of instruments Bohannon J Science in Libya. Evidence overruled: medics on death row. Science. 2005 Apr 8;308(5719):184-5. Court overrules scientific evidence Libyan court disregarded the Western evidence and only considered the evidence from Libyan scientists that supported the claims of deliberate

infection All 6 health care workers were sentenced to death (for second time) on 19 Dec 2006 for deliberately infecting children The Libyan scientists arguments were based on a poor understanding of phylogenetics and a premise of discounting that the poor infection control could account for such a large outbreak Libyan Journal of Medicine (O. Bagasra 2007) Advanced phylogenetics to the

rescue de Oliveira, Tulio, et al. Molecular Epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature 444.7121 Methods HIV-1 gag gene sequences from 44 children 61 Hepatitis C Virus E1E2 gene

sequences Phylogenies were estimated and assessed using algorithmic, Bayesian and maximum-likelihood methods NATURE Vol 444: 14 December 2006 Results HIV-1 sequences: Monophyletic cluster within

CRF02_AG (a circulating recombinant form of HIV) The cluster is closest to West African reference strains HCV sequences: Three monophyletic clusters - related to Egyptian 4a strains Evolution was analysed using an established Bayesian Markov chain Monte Carlo approach Irrespective of model used the most recent common ancestor predated March 1998 when the accused HCWs arrived at the Al-Fateh Hospital

It suggested that the Al-Fateh Hospital had a long-standing infection control problem NATURE Vol 444: 14 December 2006 NATURE Vol 444: 14 December 2006 NATURE Vol 444: 14 December 2006

NATURE Vol 444: 14 December 2006 Phylogenetics in Forensics Importance of established methodology Timing of transmission events Model bias could be excluded by concordance of different models The importance of clusters in providing evidence of common source outbreaks!

The aftermath of the Libyan case Accused were sentenced to death for the second time in 19-Dec-2006 Extradited to Bulgaria, where they were later released Libya complained about the release In February 2011 the resigned minister Mustafa AbdelJalil alleged that Gaddaffi and his government were entirely responsible for the infection of the children with HIV

The reason for the extremely high rate of transmission has not been resolved in literature but is not inconceivable (HIV transmission is highly variable and dependant on viral load and nature of exposure) Sofia airport: Bulgarian president Georgi Parvanov pardons the medical team convicted of infecting Libyan children with HIV. Declan Butler. Libyan ordeal ends: medics freed. Nature

448, 398 (26 July 2007) Published online 25 July 2007 References

Moszynski P. Outrage over death sentences in Libyan AIDS trial. BMJ. 2007 Jan 6;334(7583):11. Yerly S, Quadri R, Negro F, Barbe KP, Cheseaux JJ, Burgisser P, Siegrist CA, Perrin L. J Infect Dis. 2001 Aug 1;184(3):369-72. Epub 2001 Jul 10. Omar Bagasra, Mohammed Alsayari, Rebecca Bullard-Dillard and Mohamed A Daw. The Libyan HIV Outbreak: How do we find the truth? Libyan J Med 2007

Bohannon J Science in Libya. Evidence overruled: medics on death row. Science. 2005 Apr 8;308(5719):184-5. de Oliveira, Tulio, et al. "Molecular Epidemiology: HIV-1 and HCV sequences from Libyan outbreak." Nature 444.7121 Declan Butler. Libyan ordeal ends: medics freed. Nature 448, 398 (26 July 2007) Published online 25 July 2007 Case 3 Influenza: Phylogenetics,

evolution and selection pressure ssRNA in 8 segments highly mutable (lack of

proofreading by RNA polymerase) Picture by Prof Wolfgang Preiser Annual influenza Three influenza strains are causing annual epidemics

Influenza uses haemagglutinin (HA) to bind to and infect cells in the patients airway, whereas neuraminidase (NA) plays a role in release from the mother cells to infect a new generation of cells. When the host (human) forms antibodies against HA and NA proteins these could prevent the virus from infecting cells Immunity towards influenza is based on these neutralising antibodies

After each seasonal epidemic many people who became infected have neutralising antibodies and are therefore not susceptible to the circulating strain(s) Immune pressure

There is immune system selection pressure on the HA and NA genes Mutations in HA or NA could either be detrimental limit the fitness of the virus or be beneficial by resulting in escape from antibody pressure

Some variants that are both fit and have the ability to escape the immune pressure have a survival advantage There is therefore selection for and enrichment for these immune escape variants During summer there are only few cases of influenza infection (transmission rates are lower than in winter) Therefore only a few variants survive the combined immune pressure and unfavourable conditions during summer (or are reintroduced from other countries during the following winter season) Influenza viruses therefore evolve along various bottle-necks and

expand again during a favourable winter season Figure: Immune escape of influenza viruses Evolutionary bottle-neck Immune pressure AND unfavourable conditions

Time Original viral population Immune escape variants after selection Influenza Phylogenetic

Tree TIME Bush RM, Bender CA, Subbarao K, Cox NJ, Fitch WM. Predicting the evolution of human influenza A. Influenza exposed to frequent bottlenecks Influenza phylogenetics are used to decide on the selection of each years vaccine strains (in

order to give the best immune protection) How does the influenza tree compare to the HIV1 CRF02_AG tree in case 2? What kinds of pressures are infectious agents exposed to? Host immunity Functional and structural constraints Anti-infective drug pressure Where on the tree do you find the old versus the

current circulating strains? References Frank SA. Immunology and Evolution of Infectious Disease. Princeton(NJ): Princeton University Press; 2002 Bush RM, Bender CA, Subbarao K, Cox NJ, Fitch WM. Predicting the evolution of human influenza A. Science. 1999 Dec

3;286(5446):1921-5. Li W, Shi W, Qiao H, Ho SY, Luo A, Zhang Y, Zhu C. Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses. Virol J. 2011 Apr 21;8:183. Thank You Questions?

Recently Viewed Presentations

  • basic biochemical processes on living things

    basic biochemical processes on living things

    TWO BIOCHEMICAL PROCESSES ASSOCIATED WITH ENERGY IN LIVING THINGS ARE: PHOTOSYNTHESIS. CELLULAR RESPIRATION. PHOTOSYNTHESIS. The process by which autotrophs store the Sun's energy in ORGANIC molecules such as carbohydrates. respiration.
  • Analytical Reading Inventory - Santee School District

    Analytical Reading Inventory - Santee School District

    Analytical Reading Inventory Grades 4-8 What? The ARI is an informal, individualized reading inventory. This inventory will allow you to analyze decoding, fluency, and comprehension. Who? All students grades 4-8 who scored 325 or below on ELA CST. Grade 2-8...
  • YMCA of Regina Strategic Plan June 2013 YMCA

    YMCA of Regina Strategic Plan June 2013 YMCA

    We will strive to be the premier values-based builder of health, leadership and personal development. Values: Honesty, Caring, Respect, Responsibility, Inclusiveness. ... Members include the YMCA in their Wills and Estates planning and view us as a charity.
  • Canadas national centre for particle and nuclear physics

    Canadas national centre for particle and nuclear physics

    TRIUMF Facilities . 500 MeV 400 uA proton cyclotron. 2 - 100 uA beamlines (meson, RIB) 1 - Medical isotope production 100 MeV and 100 uA. 50 MeV, 500 kW e-Linac
  • Poetry Analysis - Mrs. Belof's classes

    Poetry Analysis - Mrs. Belof's classes

    What is TP CASTT? An acronym of steps used to analyze poetry. The results of TPCASTT can be used to write an essay. The TPCASTT process is comprised of 7 steps which should be completed in the order given.
  • Darwin's Theory of Evolution The Puzzle of Life's Diversity ...

    Darwin's Theory of Evolution The Puzzle of Life's Diversity ...

    Title: Darwin's Theory of Evolution The Puzzle of Life's Diversity Chapter 15-1 Author: Becca Riedell Last modified by: Kelly Riedell Created Date
  • A Corresponding Study of Water Quality Evaluation of the ...

    A Corresponding Study of Water Quality Evaluation of the ...

    A Continuing Study of Water Quality in the Pasquotank Watershed in Northeastern North Carolina. Research Experience for Undergraduates in Ocean, Marine, and Polar Science. Elizabeth City State University June 1- July 29,2016
  • Specialty Team Advising Research (STAR)

    Specialty Team Advising Research (STAR)

    A CRADA is an agreement established pursuant to the Federal Technology Transfer Act of 1986, Public Law (Pub. L.) 99-502 between Department of Veterans Affairs (VA) and one or more non-Federal, and Federal parties under which VA may accept, retain...