Skip main navigation

How to prevent sequencing and sampling bias

In this video a specialists discusses the potential sampling biases and how to prevent them

In this video, Dr Catherine Ludden talks about sampling strategies that can prevent biases which can impact public health actions.

When deciding which samples to sequence, there are many options depending on the capacity of your network, the stage of the pandemic in your country and the most pressing public health questions requiring answers. Figure 1 shows some different categories of samples and one way of thinking about prioritisation.

Whilst these priorities will be different in each setting, it is almost universally accepted that the most important and primary activity in genomic surveillance is the tracking of different lineages and variants. This is best achieved by taking a random, unbiased and geographically representative sample of cases. This approach will be informative as to the lineages circulating, potentially at low levels depending on the size of the sample.

Sampling in hospitals, intensive care units, suspected imported cases, and care homes can answer very important targeted public health questions but, without being accompanied by general surveillance, risks a bias in the data.

Illustrative pyramid indicating potential categories of types of samples. In the base “targeted variant tracking examples: borders, community surveys, wastewater samples, vaccine trials and therapeutic trials” are considered. The middle section is for surveillance of transmission: hospitals, care homes, schools and prisons. The top section, i.e. the smaller proportion of sequencing, is destined for untargeted variant tracking, covering any other site not mentioned in the other categories.

Click to enlarge

Figure 1 – An example of some potential categories of public health options and the types of samples you might decide to sequence.

This article is from the free online

A Practical Guide for SARS-CoV-2 Whole Genome Sequencing

Created by
FutureLearn - Learning For Life

Reach your personal and professional goals

Unlock access to hundreds of expert online courses and degrees from top universities and educators to gain accredited qualifications and professional CV-building certificates.

Join over 18 million learners to launch, switch or build upon your career, all at your own pace, across a wide range of topic areas.

Start Learning now