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Transmission detection: travel-associated, hospital and community transmission

Case studies where genomic data was used to distinguish hospital SARS-CoV2 spread from community spread, and to study travel-associated transmission
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The clinical spectrum of coronavirus disease 2019 (COVID-19) infection is wide, ranging from asymptomatic infection to severe viral pneumonia leading to death. SARS-CoV-2 is highly transmissible by droplet and indirect contact. Viral load in asymptomatic patients may be similar to those who are symptomatic.

Schematic illustration of transmission of asymptomatic COVID-19 patients. The asymptomatic patient is the source of the transmission. They transmit it to one family and start a second transmission route in a hospital. One of the people in the hospital, then transmits the virus to a second family

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Figure 1- Transmission of asymptomatic COVID-19.

Health care workers (HCWs) may be a source of infection for patients and colleagues via asymptomatic carriage and transmissibility prior to the onset of symptoms. Studies describing the risk and events of SARS-CoV-2 intra-hospital transmission are discrepant.

During an epidemic, when there is frequent viral transmission in the community, it is not always clear whether the patients are infected due to local transmission or through the HCWs. As the pandemic is constantly evolving, a new awareness of specific variants has soared from fear of strains more transmissible, pathogenic and likely to evade immunisation efforts. As outbreak definitions vary and outbreak reports mainly depend on epidemiological data with SARS-CoV-2 test results, the true transmission patterns remain uncertain. An aggregation of infected HCWs in a ward over some days or weeks does not necessarily imply intra-hospital transmission or a local outbreak.

A study conducted by Francis and colleagues at Nottingham University Hospitals Trust showed how they were able to detect how the intra-hospital transmission of COVID-19 infections occurred. They subjected all samples from patients as well as staff to reverse-transcription polymerase chain reaction (RT-PCR). Samples with a positive RT-PCR result (with a cycle threshold of < 35) and suggestive epidemiological linkage were subjected to whole-genome sequencing. The SNP analysis of these samples revealed that there were multiple outbreaks which occurred during the study period (Figure 2). They could differentiate the outbreaks by identifying the uniqueness of the samples such as common lineage detection, unique mutations, timeline analysis etc.

T at position 12052″>

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Figure 2 – The position highlighted in red at position 12052 shows that the mutation G>T is a marker which was used to distinguish between the outbreak isolates and the community samples. This study by Francis et.al concluded that this outbreak started through an asymptomatic patient and further spread through HCW to the patients in the ward who carried the same mutation and belonged to B.1.1.17 variant. Source: The Journal of Infectious Diseases

A similar kind of study can be conducted with cases having a history of travel. It is very evident throughout that there is a direct link between infection and travel history. Phylogenetic studies can help us identify the route of transmission so that as far as possible appropriate travel restrictions and quarantine measures can be adopted to control the virus spread (Figure 3). To understand it in detail you can refer to an article by Oude Munnink and colleagues where they have conducted phylogenetic analysis on cases with travel history in the Netherlands to understand the transmission.

Visit Nextstrain and explore the tool. Can you identify the predicted transmission route for the SARS-CoV-2 variants in your country? Share your interpretation in the comments.

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Making sense of genomic data: COVID-19 web-based bioinformatics

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