Notable omissions and deviations

The detailed steps in §3.3 describe the process followed from execution of the literature search protocol to capturing the information in the literature instances to the dataset. There are, however, some notable omissions to and deviations from these steps. The omissions are described in §3.4.1 followed by a description of the deviations in §3.4.2. The sections which the omissions and deviations are relevant to are tabulated in Table 3.6.

3.4.1 Omissions

An explanation of the notable omissions tabulated in Table 3.6, as well as a rationale for the omissions, is provided below.

Transmission modes omitted from structured literature review

Diseases which are transmissible by means of animal and soil contact are not included within the review.4 _{It is very unlikely that these transmission modes would lead to an epidemic outbreak, as}

sustained contact with animals and soil are required to ensure continuous propagation of the disease. However, one potential exception is that of anthrax. Two reasons for the exclusion of this disease are the following:

 Most examples of anthrax modelling efforts focus on transmission between animals; and  The few examples of anthrax transmission modelling between humans relate to very specific

examples of bioterror attacks and are not considered for generalised population-level disease modelling (one example is (Wanying et al. 2016) ).

RI diseases and non-RI diseases not included

A complete list of the diseases which are not included in the structured review, as well as a reason for each omission, is provided in Table 3.7.

Pay-per-view articles

On average, the proportion of the pay-per-view articles amounted to 11.9% of the ‘potential abstracts’ literature instances. The maximum percentage of articles not available for a given disease are 20% of the total potential literature instances. The typical price for a pay-per-view article amounts to 30 US$. In order to obtain access to these additional articles, an estimated 1 950 USD$ would be required, which equals to R23 400 at a conservative exchange rate of 12 ZAR / 1 USD$. The number of literature pieces that are available free of charge through the Stellenbosch University license are

deemed sufficient to eliminate the need to acquire funding to access the pay-per-view articles. The number of pay-per-view articles for each disease is produced in §C.2.

Referencing literature uncovered during the iterative filtering process in the bibliography As part of the iterative filtering process, the number of potential literature instances are noted for each of the steps. Only the final number of ‘relevant articles’ for each disease are referenced in Appendix H. Thus, none of the potential literature instances which are eliminated in the iterative filtering process are included in this reference list.

Table 3.7: Rationale for omission of particular diseases from the structured review.

Disease Reason for omission

Hepatitis B (RI)

Hepatitis is a disease which causes inflammation of the liver (WHO 2016b). Even though Hepatitis B is included within the vaccine schedule, the incubation period which ranges between 60 and 90 days (GIDEON 2017a) is considerably longer than the incubation cut- off time of 30 days specified in §3.2.2.

HIV (non-RI)

Although HIV is one of the more frequently modelled sexual and body fluid transmissible diseases, the unusually long incubation period which varies between 60 days and 10 years (GIDEON 2017a) falls outside the scope as specified in §3.2.2.

HPV (RI)

The various strains of HPV are known to cause diseases which range in severity from warts (short incubation period between 2 weeks and 8 months) to various cancers in both males and females (GIDEON 2017a). As the focus of this study is on specific communicable diseases, HPV related modelling and diseases are considered to fall outside the scope of the review.

Influenza type B (RI)

As the H1N1 strain of influenza is already included within the study, the inclusion of an additional influenza strain is deemed superfluous.

Pneumococcal (RI)

The pneumococcal vaccine targets general respiratory bacteria, therefore there isn’t a specific disease that is associated with the vaccine and for which the spread through a population can be modelled (GIDEON 2017a).

Tuberculosis (RI)

Even though the study of the modelling of TB is an important research field, especially due to the presence of multiple drug resistant strains, the long incubation period which varies between 28 and 84 days (GIDEON 2017a) falls outside the scope of this study as specified in §3.2.2.

Tetanus (RI)

Tetanus is a disease transmitted by means of contact with contaminated objects such as rusty metallic objects. As this disease is transmitted in extremely rare cases (only transmissible by a vehicle described as trauma (GIDEON 2017a) ) it is not considered within the review.

3.4.2 Deviations

An explanation of the notable deviations tabulated in Table 3.6, as well as the rationales for the deviations, are provided below.

Additional keyword exclusion

As tabulated in Table C.4, the number of potential articles for three of the diseases following categorical exclusion are:

 H1N1 (1489);  Malaria (3131); and  Dengue (1399).

The total number of potential literature titles requiring review for these three diseases add up to 6019 instances, which amounts to 46% of the potential literature instances for this step of the iterative filtering process. It is deemed unnecessary to devote nearly 50% of the literature title review workload to three disease instances. To reduce the number of potential titles, an additional keyword exclusion was performed on the three aforementioned diseases. The complete list of keywords included in the deviant Scopus search protocol is reproduced in §C.1.9 (dengue), §C.1.11 (H1N1) and §C.1.12 (malaria).

Additional timeframe exclusion

As tabulated in Table C.4, following the additional keyword exclusion, the revised number of potential literature titles for two of the diseases following the additional keyword exclusion are:

 Malaria (1581); and  Dengue (818).

The total number of potential titles for these three diseases add up to 2399 instances, which amounts to 22% of the literature title review step. It is deemed unnecessary to devote nearly 25% of the literature title review workload to two disease instances. To further reduce the number of potential literature instances included in the review process, an additional timeframe exclusion is performed on these two diseases. This timeframe is selected to only consider literature instances published between 2015 and 2017. The reason for not including H1N1 in the additional timeframe exclusion is that a major outbreak of H1N1 occurred between 2009 and 2010, as illustrated in Figure 1.2. The deviant Scopus search protocol for dengue and malaria following the timeframe exclusion is reproduced in §C.1.9 and §C.1.12, respectively.

Mathematical vs simulation approach classification

Some mathematical modelling approaches (e.g. linear programming approaches) stated that results are ‘simulated’ with different parameters. This is not regarded as true stochastic simulation (as discussed previously in §2.3.4) and is still regarded as a mathematical modelling approach.

Mixing pattern capturing logic

In some literature pieces, the assumption of homogeneous mixing is mentioned. As homogeneous is regarded as the default mixing pattern, an article was only marked as incorporating alternative mixing patterns if non-standard mixing patterns were mentioned and incorporated in the modelling approach.