Genomic Epidemiology of SARS CoV 2 Sequencing in Pakistan

Genomic Epidemiology of Novel Coronavirus - Pakistan and Related Contextual (Targeted) Samples

This tree is designed to facilitate outbreak investigation, where typical questions include: are all these samples actually part of the outbreak? Did the outbreak originate from a single introduction event? Has an outbreak been contained to the localized setting or did it spill over and circulate within the wider community. For these types of investigations, it is critical to take into account the broader viral diversity of a region as a reference for the outbreak when making epidemiology interferences. To facilitate that, we added to the tree contextual samples that are most closely related to the Pakistan samples. These contextual samples will include samples that are unrelated to the users selected samples, but are collected over time across global regions to provide a more accurate estimate of the evolutionary rate.

Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/Non-targeted)

The non-contextualized tree is designed to provide an overview of samples collected only from within the user's jurisdiction, e.g., Pakistan. This tree lacks contextual data that are crucial for making sound epidemiological interferences, and thus we caution against its use for any purpose other than simply looking at viral diversity across the jurisdiction. This trees shows all the samples collected within a user's jurisdiction by including data from GISAID. In this way, it may help a user to diagnose whether certain populations sampled by other groups show different patterns of viral diversity than what the user has captured across their own samples, where they may help a user in assessing whether their samples are preferentially sampling certain viral lineages circulating in their jurisdiction.

Depending on the number of total samples collected in the jurisdiction either by the user or by other groups, some samples may be left out of the tree to ensure a tree size that is viewable and interpretable (around 2,000 samples). If any samples are of particular interest based on the specific use case, select these samples for the tree build to force them to be included in the tree. Note that user-selected samples will not be subjected to the same temporal subsampling as the other samples, so if the user selection is of a large number, it may bias the proportions of the lineages on the tree. Other samples are not selected based on their relationship to user-selected samples, as opposed to the tree type in the previous section.