Module 1: Answers to Activity Questions
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Answers to Questions in Module 1.1
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Here are the answers to the questions in Module 1.1:

#. There is a lot of under-reporting of cholera cases (`Ali et al 2015`_, `Hegde et al 2024`_). In the MSF video, they say it is estimated that only 5-10% of cholera cases are reported to the WHO each year.
#. The MSF video says that in endemic areas, healthy carriers far exceed the percent of people who show symptoms (upon infection with the current pandemic lineage of *V. cholerae*, ie. the 7PET lineage). That it, it is estimated that most people who are infected with the 7PET lineage are asymptomatic (`Nelson et al 2009`_). The percent of people who develop symptoms (e.g. acute watery diarrhoea) probably varies a lot between populations, as populations that have suffered recent outbreaks caused by 7PET likely have greater immunity (`Bencić & Sinha 1972`_, `Nelson et al 2009`_). Asymptomatic carriage is likely responsible for considerable regional and global transmission of the 7PET lineage (`King et al 2008`_, `Islam et al 2017`_).
#. The video by the IAQ video Network says that there have been outbreaks of diarrhoeal illness caused by eating shellfish (containing non-epidemic *V. cholerae*) from the Gulf of Mexico region of the USA. For example, `Haley et al 2014`_ described a small outbreak of 11 cases of diarrhoeal illness caused by consumption of oysters (containing non-epidemic *V. cholerae*) from the Gulf of Mexico region of the USA. Several different lineages of non-epidemic *V. cholerae* have been identified in the coastal waters of the Gulf of Mexico; one of these lineages was even  named 'Gulf Coast' because it was first isolated from the Gulf of Mexico (see Figure 6 in Module 1.1; `Kaper et al 1982`_, `Domman et al 2017`_).
#. The length of protection after infection with cholera is a subject of ongoing scientific research; it may depend on the severity of the previous infection, and on how similar the *V. cholerae* causing new infection is to the *V. cholerae* that caused the previous infection in its genes for key antigens (`Leung & Matrajt 2021`_, `Harris 2018`_). In the interview with Dr Qadri, she says that a person who suffers from *severe* cholera is protected from reinfection for approximately 7-10 years. `Harris 2018`_ says there is strongest evidence for protection for the first 3 years after a cholera infection, and that the length of protection may depend on whether the *V. cholerae* causing new infection is the same or different in its genes for key antigens compared to the *V. cholerae* that caused the previous infection. 
#. In the interview with Dr Qadri, she says that the current oral cholera vaccines are 60-70% efficacious. 

.. _Leung & Matrajt 2021: https://pubmed.ncbi.nlm.nih.gov/34014927/

.. _Ali et al 2015: https://pubmed.ncbi.nlm.nih.gov/26043000/

.. _Hegde et al 2024: https://pubmed.ncbi.nlm.nih.gov/38378884/

.. _Bencić & Sinha 1972: https://pubmed.ncbi.nlm.nih.gov/4669174/

.. _Nelson et al 2009: https://pubmed.ncbi.nlm.nih.gov/19756008/

.. _Islam et al 2017: https://pubmed.ncbi.nlm.nih.gov/29446801/

.. _King et al 2008: https://pubmed.ncbi.nlm.nih.gov/18704085/

.. _Kaper et al 1982: https://pubmed.ncbi.nlm.nih.gov/7107852/ 

.. _Harris 2018: https://pubmed.ncbi.nlm.nih.gov/30184117/

.. _Haley et al 2014: https://pubmed.ncbi.nlm.nih.gov/24699521/

.. _Domman et al 2017: https://pubmed.ncbi.nlm.nih.gov/29123068/

Answers to Questions in Module 1.2
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Answers to Questions in Module 1.3
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Answers to Questions in Module 1.4
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Vibriowatch
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In later modules of this course, you will learn how to carry out bioinformatics analyses using `Vibriowatch`_, as well as other bioinformatics tools.
If you already have cholera genomic data to analyse, and want to get going quickly, you may also be interested in our `Vibriowatch`_ tutorial.

.. _Vibriowatch: https://vibriowatch.readthedocs.io

Contact
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I will be grateful if you will send me (Avril Coghlan) corrections or suggestions for improvements to my email address alc@sanger.ac.uk

Acknowledgements
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Contributors to this course: Avril Coghlan, Matt Dorman, Ismail Bashir, Anne Bishop, Amber Barton, Stephanie McGimpsey, Jolynne Mokaya, Nisha Singh, Nick Thomson.