Lower Respiratory Infections: GBD 2017

Disease Description

Lower respiratory infections (LRI), principally clinician-diagnosed pneumonia and bronchiolitis, is a major global killer of both children and adults. Symptoms include shortness of breath, weakness, fever, coughing and fatigue. It is important to check for a fever. Symptoms can last about 7 days and the infection is contagious to others shortly before and while experiencing symptoms. It is mainly caused by four pathogens - Streptococcus pneumoniae (pneumococcal pneumonia), Haemophilus influenzae type B (Hib), influenza, and respiratory syncytial virus (RCV). Those pathogens may co-infect. Pneumococcal pneumonia is the largest cause of LRI mortality. [Wikipedia-LRI], [GBD-2017-YLD-Capstone-Appendix-1-lri]

The lower respiratory tract or lower airway is derived from the developing foregut and consists of the trachea, bronchi (primary, secondary and tertiary), bronchioles (including terminal and respiratory), and lungs (including alveoli). It also sometimes includes the larynx. [Wikipedia-LRI]

Transmission of LRI may occur via several pathways, including direct physical contact, fomites, direct droplet spread, and suspended small particles. Intermingling of large numbers of people can facilitate transmission of respiratory pathogens. [CDC-LRI]

In GBD 2016, malnutrition was identified as a leading risk factor for lower respiratory infection mortality among children younger than 5 years and, together with air pollution (both household and ambient) and increased antibiotic use, was identified as a focus for targeted intervention measures. [Lancet]

Todo

Describe more about deaths and complications due to LRI. Talk about current vaccination against influenza and pneumonia. https://apps.who.int/iris/bitstream/handle/10665/241904/WER8714_129-144.PDFp

Modeling LRI in GBD 2017

The GBD 2017 defined the time to recovery for LRI as an average of 10 days (5-15 days), which corresponds with a remission 36.5.

Todo

Describe more about modeling LRI in GBD 2017

GBD hierarchy

../../../../_images/lri_hierarchy.svg

c_{} - cause_{gbd_id}, s_{} - sequelae_{gbd_id}

GBS stands for Guillain-Barré syndrome.

Cause Model Diagram

../../../../_images/lri_disease_model.svg

Model Assumptions and Limitations

This model is designed to be used for estimating DALYs due to LRI that are averted from a country-level intervention(e.g. food fortification or supplementation given to a percentage of the population) that can reduce LRI incidence as a downstream effect.

There is substantial additional effort in GBD to divide LRI burden into the aetiologies of LRI, but we do not include aetiologies in this simple model.

There are three sequelae associated with LRI. We are not tracking the long-term effects of Guillain-Barré syndrome (which can include paralysis, for example). However, since the prevalence of GBS is so low, there would probably not be much benefit in attempting to capture its long-term YLDs in addition to its short term YLDs.

Note

Birth prevalence of LRI was allowed in the DISMOD modeling process for LRI. However, it was not reported as a final result in GBD 2017. LRI birth prevalence must therefore be retreieved using get_model_results(‘epi’, 1258, age_group_id=164, measure_id=5, gbd_round_id=5, year_id=2017) or get_draws(‘modelable_entity_id’, 1258, source=’epi’, age_group_id=164, measure_id=5, gbd_round_id=5, year_id=2017).

Todo

Describe more assumptions and limitations of the model.

Data Description

Definition

State

State Name

Definition

S

Susceptible

Susceptible but does not currently have LRI

I

Infected

Currently infected and having the condition
States Data

State

Measure

Value

Notes

S

birth prevalence

1-birth_prevalence_meid1258

S

prevalence

1-prevalence_c322

S

excess mortality rate

0

S

disability weights

0

I

birth prevalence

birth_prevalence_meid1258

I

prevalence

prevalence_c322

I

excess mortality rate

\(\frac{\text{deaths\_c322}}{\text{population} \,\times\,\text{prevalence\_c322}}\)

I

disability weights

disability_weight_s670 \(\times\) prevalence_s670+ disability_weight_s669 \(\times\) prevalence_s669 + disability_weight_s671 \(\times\) prevalence_s671

ALL

cause specific mortality rate

\(\frac{\text{deaths\_c322}}{\text{population}}\)
Transition Data

Transition

Source

Sink

Value

Notes

i

S

I

\(\frac{\text{incidence\_rate\_c322}}{(1-\text{prevalence\_c322})}\)

Incidence in GBD are estimated for the total population. Here we transform incidence to be a rate within the susceptible population.

r

I

S

remission_rate_c322
Data Sources

Measure

Sources

Description

Notes

birth_prevalence_meid1258

epi

Birth Prevalence of LRI

get_draws(‘modelable_entity_id’, 1258, source=’epi’, age_group_id=164, measure_id=5, gbd_round_id=5, year_id=2017)

prevalence_c322

como

Prevalence of LRI

deaths_c322

codcorrect

Deaths from LRI

population

demography

Mid-year population for given age/sex/year/location

incidence_rate_c322

como

Incidence rate of LRI within the entire population

remission_rate_m1258

dismod-mr

Remission rate of LRI within the infected population

disability_weight_s{sid}

YLD Appendix

Disability weights associated with each sequela

Note Guillain-Barre due to LRI is included in sequelae.

prevalence_s{sid}

como

Prevalence of each sequela with id ‘sid’
Restrictions

Restriction type

Value

Notes

Male only

False

Female only

False

YLL only

False

YLD only

False

YLL age group start

Early neonatal

GBD age group id is 2

YLL age group end

Age 95+

GBD age group id is 235

YLD age group start

Early neonatal

GBD age group id is 2

YLD age group end

Age 95+

GBD age group id is 235

Validation Criteria

Baseline vivarium model results should compare to GBD artifact data with respect to age-, sex-, location-, and year-specific LRI:

  • Birth prevalence

  • Prevalence

  • Incidence rate

  • Remission rate

  • Cause-specifc mortality rate

  • Excess mortality rate

  • YLDs due to LRI

  • YLLs due to LRI

Note

The prior bound for the LRI remission rate is 7.3 days, which is longer than the duration of the early neonatal age group (6 days), so theoretically there should be few or no remitted cases of LRI in the early neonatal age group. However, LRI birth prevalence is expected to be greater than LRI prevalence in the early neonatal age group due to LRI’s excess mortality rate.

References

[Wikipedia-LRI] (1,2)

Lower respiratory tact infection. From Wikipedia, the Free Encyclopedia. Retrieved 22 Nov 2019. https://en.wikipedia.org/wiki/Lower_respiratory_tract_infection

[CDC-LRI]

Respiratory Infections (The Yellow Book). Centers for Disease Control and Prevention, 2019. Retrieved 20 Dec 2019. https://wwwnc.cdc.gov/travel/yellowbook/2020/posttravel-evaluation/respiratory-infections

[Lancet]

The Global Burden of Lower Respiratory Infections: Making Progress, but We Need to Do Better (Volume 18). The Lancet Infectious Diseases, 2018. Retrieved 20 Dec 2019. https://www.sciencedirect.com/science/article/pii/S1473309918304079?via%3Dihub