viral epidemiology

Question 1

HIV-1 incidence

Answer 1

• jumped from chimpanzees to humans in the late 19th century in central africa
• diversified within central arica for at least 50 years before achieving a consistent spread over the continent
• spread to Haiti in the 1960’s, then New York in the 70s, then radiated across the western world

Question 2

West Nile virus

Answer 2

• first detected in Africa but since spread across the world
• caused alarm in the US around 1999/2000
• a variant is now spreading across europe and is expected in the UK soonish

Question 3

Zika virus incidence

Answer 3

• first detected in Uganda 1947
• sporadic cases in humans and wild primates were reported across Africa in the 60s to 80s
• Isolated in Malaysia in ‘66
• outbreak on a pacific island (Yap) in 2007 (only 14 confirmed cases in literature up until 2007)
• spread across the pacific in 2013, reaching the Americas by 2015
• major outbreak in Brazil
• brazilian Zika then appeared in West Africa

Question 4

What is R?

Answer 4

1 cases leads to ‘R’ cases on average

Question 5

Ps = ??

Answer 5

proportion susceptible

Question 6

Pst = ??

Answer 6

proportion susceptible at time = t

Question 7

Rt = ??

Answer 7

R0 x Pst

Question 8

Pr = ??

Answer 8

1 - proportion susceptible

Question 9

Prt = ??

Answer 9

proportion resistant at time = t

Question 10

HET = ??

Answer 10

Herd immunity threshold
HET = (R0 -1)/R0

Question 11

VE = ???

Answer 11

vaccine efficacy = the percentage of those vaccinated who are resistant

Question 12

Porportion to vaccinate to achieve herd immunity = ???

Answer 12

HET/VE

Question 13

How R changed through covid?

Answer 13

Early attempts to calculate R0 produced very different results.
Acquisition of immunity was not total in covid survivors
vaccine efficacy disappointing
New variants with higher R0
months passed and HET was never reached
superspreaders exist