SARS-COV2 COVID-19 Pathogenesis & testing Professor Omu ...

SARS-COV2

COVID-19

Pathogenesis & testing

Professor Omu Anzala

KAVI-Institute of Clinical Research

University Of Nairobi

4/23/2020Professor. Omu Anzala

VIRAL DISEASES OF THE RESPIRATORY TRACT

• Most common afflictions of humans and most are caused by viruses.

• There are about 200 human respiratory viruses, mainly within six families:-

1. Orthomyxoviruses

2. Paramyxoviruses

3. Picornaviruses

4. Coronaviruses

5. Adenoviruses

6. Herpes

ONE- HEALTH

Corona’s

bats are believed to be the ancestral host of all

the known coronavirus lineages with

transmission to animals, birds and humans

Coronaviruses

Virology

• Large –enveloped

• Positive-stranded RNA

• Replicates in Cytosol

• High frequency of recombination during

replication

Coronaviruses

Natural Hosts

• Humans

• Pigs

• Dogs

• Cats

• Camels

• Bats

• Snakes

• Birds

Coronaviruses

Human Coronas

• HCoV-229E

• HCoV-OC43 Endemic world-wide

• HCoV-NL63

• HCoV-HKUI

• MERS-CoV - 2012-2013 (2500 cases,800 deaths,

Middle East )

• SARS CoV - 2002-2003 (8098 cases,774 deaths,

Mainland china & Hong Kong

Receptor Recognition

Viral receptor recognition is a major determinant of :

• Host range

• Cross-species infections

• Pathogenesis

SARS-COV & SARS-COV-2

Host cell Recognition

• Ligand – spike protein on viral envelope

• Receptor – Angiotensin –converting enzyme-2 (

ACE2)

• Wide distribution of ACE2 in human organs ( Heart,

Kidney, Lung both on epithelial and Endothelial surfaces )

SARS-COV-2

(COVID-19)

Samples

• Respiratory Secretions

• Stool

• Urine

• Blood

Culture, Serology, RT-PCR

Currently Available Diagnostic Assays

Molecular Diagnostic Assays

• Berlin Protocol

Qualitative Real Time RT-PCT

Targets ( E gene and RdRp gene)

• CDC Protocol

Qualitative Real-Time RT-PCR

Target ( N gene )

Tests Under Development

• Rapid Molecular test

• Rapid serology test

Feaces- 44%

positive late in

disease

Maybe one

source to catch

the viral RNA,

but what about

transmission ??

CoV- Pathogenesis

• Initial infection targets epithelial cells lining the upper

respiratory tract

• Viruses then spread to the lower respiratory tract

- Bronchitis

- Bronchiolitis

- Pneumonia

- CNS ??

( Viremia ??)

SARS-

CoV-2: A

Storm is

RagingSavannah F.

Pedersen,

Ya-Chi HoJ Clin Invest. 2020.

https://doi.org/10.1172/JCI1

37647.

ACE2 and COVID-19

Could there be a correlation between ACE2 and

disease out come?

distribution of ACE2 receptors in the respiratory

tract?

Expression of ACE2 receptors in the different

age groups ( Epigenetics)?

One Health Zoonotic Diseases Project

(Taita, Kibira,Busai Research Sites)Objectives:- To determine prevalence and patterns of ZAIs in patients with acute febrile illness

- To determine the prevalence of zoonotic and arboviruses in bats, rodents and mosquitoes

- To identify any novel/emerging pathogens in patients with acute febrile illness in the study areas

-To identify potential biomarkers and/or immunogens for common ZAIs.

Species of bats trapped in 2019

Species Taita Busia CoV Prev

1 Mops condylurus 221 106 3.7 (12)

2 Chaerofon pumilas 177 18 22.1(43)

3 Rhinolophus sp. 2 -

4 Coleura afra - 19 -

5 Epomophoruslabiatus

- 31 12.9 (4)

6 Neoromicia nana 1 -

Total 400 176 10.2 (59)

MERS-CoV antibodies by ELISA in dromedary camels from 13 counties in Kenya, 2016

Region County Breed Tested

camels

No. of

positive

Positive rate, % (95%

CI)

A Turkana Turkana 74 51 68.9 (57.1-79.2)

West Pokot Turkana 67 19 28.4 (18.0-40.7)

Baringo Turkana 15 6 40.0 (16.3-67.7)

B Samburu Gabbra/ Rendille 112 90 80.4 (69.8-85.8)

Isiolo Gabbra/ Rendille 102 75 73.5 (63.7-81.8)

Marsabit Gabbra/ Rendille 79 69 87.3 (78.0-93.8)

C Mandera Somali 93 66 71.0 (60.6-79.9)

Wajir Somali 103 82 79.6 (70.5-86.9)

Garissa Somali 88 65 73.9 (63.4-82.7)

Tana River Somali 61 43 70.5 (57.4-81.5)

D Laikipia Pakistan/

Mixture

84 14 16.7 (9.42-26.4)

E Kitui Somali 14 6 42.9 (17.7-71.1)

Makueni Somali 5 2 40.0 (5.27-85.3)

Total 897 588 65.6 (62.1-68.4)

Agwanda, Ommeh, Masika et al

2020_UoN Collabo meeting 2020

Nationwide surveillance of MERS-CoV

antibodies by ELISA in humans with

exposure to camels in 10 counties in

Kenya, 2016Region County No. tested

individuals

No. positive Positive rate, %

(95% CI)

A West Pokot 41 8 19.5 (8.82-34.9)

Turkana 38 0 0.0 (0.0-9.25)

B Samburu 44 0 0.0 (0.0-8.04)

Isiolo 48 1 2.08 (0.052-11.1)

Marsabit 19 0 0.0 (0.0-17.7)

C Wajir 46 2 4.35 (0.53-14.8)

Garissa 6 1 16.7 (0.421-64.1)

Tana River 57 1 1.75 (0.04-9.40)

Mandera 18 0 0.0 (0.0-18.5)

D Laikipia 6 0 0.0 (0.0-45.9)

Total 323 13 4.02 (2.16-6.78)Agwanda, Ommeh, Masika et al

2020_UoN Collabo meeting 2020

Newly Emerging Pathogens

What we need in place:

Continues surveillance

Outbreak preparedness