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Viruses
2022 Nov 09;1411:. doi: 10.3390/v14112477.
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A National Catalogue of Viruses Associated with Indigenous Species Reveals High-Throughput Sequencing as a Driver of Indigenous Virus Discovery.
Robson M
,
Chooi KM
,
Blouin AG
,
Knight S
,
MacDiarmid RM
.
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Viruses are important constituents of ecosystems, with the capacity to alter host phenotype and performance. However, virus discovery cued by disease symptoms overlooks latent or beneficial viruses, which are best detected using targeted virus detection or discovered by non-targeted methods, e.g., high-throughput sequencing (HTS). To date, in 64 publications, 701 viruses have been described associated with indigenous species of Aotearoa New Zealand. Viruses were identified in indigenous birds (189 viruses), bats (13 viruses), starfish (4 viruses), insects (280 viruses), and plants (126 viruses). HTS gave rise to a 21.9-fold increase in virus discovery rate over the targeted methods, and 72.7-fold over symptom-based methods. The average number of viruses reported per publication has also increased proportionally over time. The use of HTS has driven the described national virome recently by 549 new-to-science viruses; all are indigenous. This report represents the first catalogue of viruses associated with indigenous species of a country. We provide evidence that the application of HTS to samples of Aotearoa New Zealand's unique fauna and flora has driven indigenous virus discovery, a key step in the process to understand the role of viruses in the biological diversity and ecology of the land, sea, and air environments of a country.
Figure 1. The cumulative viruses reported across time from 1966 to February 2022, with a specific focus on the detection method used for identification, and the number of publications in Aotearoa New Zealand indigenous hosts. ‘Total’ refers to all viruses discovered in Aotearoa New Zealand, independent of detection method. ‘Symptoms’ refers to viruses detected with symptom observation. ‘Targeted’ refers to viruses identified via targeted approaches for known viruses. ‘Non-targeted’ refers to broad-spectrum viral identification. The secondary axis in orange ‘Publications reporting viruses (cumulative)’, associated with the dotted line, refers to the number of publications reporting the viruses.
Figure 2. Total accumulated viruses reported (prior to 28 February 2022) associated with an Aotearoa New Zealand indigenous host, dependent on host type and detection method.
Figure 3. Total number of reported viruses associated with Aotearoa New Zealand indigenous hosts as of February 2022, compared based on virus status and detection method. Virus status is described in Section 2.4.
Figure 4. Total number of reported viruses associated with Aotearoa New Zealand indigenous hosts as of February 2022, compared based on identification method and viral family. Identification method refers broadly to how a virus was discovered in a New Zealand indigenous host. ‘Symptoms’ refers to viruses detected by symptom observation. ‘Targeted’ refers to viruses identified via targeted approaches with known viruses. ‘Non-targeted’ refers to broad-spectrum viral identification (for DNA viruses there are two columns, as indicated by the grey shading; the left column is a subset of the right one, which has its own scale). Viral families are split into RNA and DNA, and the hosts in which these viruses have been reported during the course of this meta-analysis have been identified via associated symbols: bats
, birds
, fish
, insects
, mollusks
, plants
, seals
, and starfish
.
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