Phylogeny and us

Phylogeny and UsPhylogeny and Us

ByPriyankar Sen, Ph.D.,Assistant Professor, CBST,VIT University, Vellore.

CASE 1CASE 1: Kimberly Bergalis: Kimberly Bergalis

•First known case of clinically-transmitted HIV

•Who was one of six patients purportedly infected with HIV by

dentist David Acer, who had AIDS.

•In December 1987, dentist Dr. David Acer removed two of

Bergalis's molars. Acer was HIV-positive at the time, having been

diagnosed that fall.

•In March 1989 Bergalis began to show symptoms of AIDS and was

diagnosed with the disease in January 1990.

• The Center for Disease Control (CDC) initial report that she had

likely acquired her infection from her dentist prompted Acer to

write an open letter requesting that his patients be tested for HIV

infection.

•The Florida health and rehabilitation service tested over 1000

patients, discovering two additional HIV-positive patients. The CDC

would eventually identify a total of ten HIV-positive former Acer

patients, and link the infections of six to their dentist.

CASE 2CASE 2: SARS 2002-03 : SARS 2002-03

INTRODUCTION

• SARS (Severe Acute Respiratory Syndrome) is a disease caused by a new type of coronavirus (SARS-CoV).

• It consists of a 29,571 base-long, single-stranded RNA and displays a characteristic spiky envelope protein that resembles a crown.

palm civet is believed to be the source of the human SARS-CoV

nucleotide sequences of 13 strains of human SARS coronaviruses for which the location and the date of collection were known

GenbankAccession CollectionDate Location ________________ ______________ ____________________

'AY278489' 'DEC-16-2002' 'GZ 12/16/02' 'AY394997' 'DEC-26-2002' 'ZS 12/26/02' 'AY395004' 'JAN-04-2003' 'ZS 01/04/03' 'AY394978' 'JAN-24-2003' 'GZ 01/24/03' 'AY394983' 'JAN-31-2003' 'GZ Hospital' 'AY304495' 'FEB-18-2002' 'GZ 02/18/03' 'AY278554' 'FEB-21-2003' 'Metropole 02/21/03' 'AY278741' 'FEB-26-2003' 'Hanoi 02/26/03' 'AY274119' 'FEB-27-2003' 'Toronto 02/27/03' 'AY283794' 'MAR-01-2003' 'Singapore 03/01/03' 'AY291451' 'MAR-08-2003' 'Taiwan 03/08/03' 'AY345986' 'MAR-19-2003' 'Hong Kong 03/19/03' 'AY394999' 'MAY-15-2003' 'Hong Kong 05/15/03' 'AY627048' ' ' 'Palm civet'

•The sequences correspond to the spike S protein, which is responsible for binding to specific receptors and is considered a major antigenic determinant.

Guangzhou and Zhongshan, labelled as GZ and ZS respectively

QUESTIONS

1. CAN PHYLOGENETIC ANALYSIS TELLS ABOUT THE SOURCE AND DYNAMICS OF AN EPIDEMIC?

2. DO IT ABLE TO TELL ABOUT THE EXACT LOCATION/PLACE FROM WHERE THE EPIDEMIC HAS SPREADED?

3. CAN IT TELL ABOUT THE EXACT DATE OF THE OUTBURST?

THE ANSWER

IS……………………..YES!!!

PAIR-WISE DISTANCES (SPIKE PROTEIN nt sequences)

Not convinced enough?...........

ON WHICH DATE IT HAS STARTED???With the help of Kimura’s Model that considers different rate of transition and transversion…..

END RESULT

SUMMARY The first cases of SARS appeared in late 2002 in the Chinese province of Guangdong.

It grew into a major outbreak in the next few months (January through February 2003).

The majority of the infected individuals acquired the disease in the Guangzhou Hospital.

A doctor who had worked in this hospital traveled to Hong Kong in February 2003 and stayed at the Metropole Hotel.

The doctor and a number of other hotel guests all became infected with the virus and traveled to different destinations (Vietnam, Canada, Singapore, Taiwan) carrying the disease and the virus.

REFERENCES:

1. https://en.wikipedia.org/wiki/Kimberly_Bergalis

2. http://in.mathworks.com/help/bioinfo/examples/

reconstructing-the-origin-and-the-diffusion-of-the-sars-

epidemic.html

3. http://www.people.com/people/archive/article/

0,,20113381,00.html

4. Centre for disease control and prevention (CDC).

THINK!!!....1. What we can do in our country……..???

2. Can we think for a entrepreneurship or socio-preneurship…………????