The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis

Objectives The SARS-CoV-2 Alpha variant was associated with increased transmission relative to other variants present at the time of its emergence and several studies have shown an association between Alpha variant infection and increased hospitalisation and 28-day mortality. However, none have addressed the impact on maximum severity of illness in the general population classified by the level of respiratory support required, or death. We aimed to do this. Methods In this retrospective multi-centre clinical cohort sub-study of the COG-UK consortium, 1475 samples from Scottish hospitalised and community cases collected between 1st November 2020 and 30th January 2021 were sequenced. We matched sequence data to clinical outcomes as the Alpha variant became dominant in Scotland and modelled the association between Alpha variant infection and severe disease using a 4-point scale of maximum severity by 28 days: 1. no respiratory support, 2. supplemental oxygen, 3. ventilation and 4. death. Results Our cumulative generalised linear mixed model analyses found evidence (cumulative odds ratio: 1.40, 95% CI: 1.02, 1.93) of a positive association between increased clinical severity and lineage (Alpha variant versus pre-Alpha variants). Conclusions The Alpha variant was associated with more severe clinical disease in the Scottish population than co-circulating lineages

Using calls as an indicator for Antarctic blue whale occurrence and distribution across the southwest Pacific and southeast Indian Oceans

Understanding species distribution and behavior is essential for conservation programs of migratory species with recovering populations. The critically endangered Antarctic blue whale (Balaenoptera musculus intermedia) was heavily exploited during the whaling era. Because of their low numbers, highly migratory behavior, and occurrence in remote areas, their distribution and range are not fully understood, particularly in the southwest Pacific Ocean. This is the first Antarctic blue whale study covering the southwest Pacific Ocean region from temperate to tropical waters (32°S to 15°S). Passive acoustic data were recorded between 2010 and 2011 across the southwest Pacific (SWPO) and southeast Indian (SEIO) oceans. We detected Antarctic blue whale calls in previously undocumented SWPO locations off eastern Australia (32°S, 152°E) and within the Lau Basin (20°S, 176°W and 15°S, 173°W), and SEIO off northwest Australia (19°S, 115°E).In temperate waters, adjacent ocean basins had similar seasonal occurrence, in that calling Antarctic blue whales were present for long periods, almost year round in some areas. In northern tropical waters, calling whales were mostly present during the austral winter. Clarifying the occurrence and distribution of critically endangered species is fundamental for monitoring population recovery, marine protected area planning, and in mitigating anthropogenic threats

Calls reveal population structure of blue whales across the Southeast Indian Ocean and the Southwest Pacific Ocean

For effective species management, understanding population structure and distribution is critical. However, quantifying population structure is not always straightforward. Within the Southern Hemisphere, the blue whale (Balaenoptera musculus) complex is extremely diverse but difficult to study. Using automated detector methods, we identified "acoustic populations" of whales producing region-specific call types. We examined blue whale call types in passive acoustic data at sites spanning over 7,370 km across the southeast Indian Ocean and southwest Pacific Ocean (SWPO) from 2009 to 2012. In the absence of genetic resolution, these acoustic populations offer unique information about the blue whale population complex. We found that the Australian continent acts as a geographic boundary, separating Australia and New Zealand blue whale acoustic populations at the junction of the Indian and Pacific Ocean basins. We located blue whales in previously undocumented locations, including the far SWPO, in the Tasman Sea off the east coast of Australia, and along the Lau Basin near Tonga. Our understanding of population dynamics across this broad scale has significant implications to recovery and conservation management for this endangered species, at a regional and global scale

Temporal Segregation of the Australian and Antarctic Blue Whale Call Types (Balaenoptera musculus spp.)

We examined recordings from a 15-month (May 2009-July 2010) continuous acoustic data set collected from a bottom-mounted passive acoustic recorder at a sample frequency of 6 kHz off Portland, Victoria, Australia (38°33′01″S, 141°15′13″E) off southern Australia. Analysis revealed that calls from both subspecies were recorded at this site, and general additive modeling revealed that the number of calls varied significantly across seasons. Antarctic blue whales were detected more frequently from July to October 2009 and June to July 2010, corresponding to the suspected breeding season, while Australian blue whales were recorded more frequently from March to June 2010, coinciding with the feeding season. In both subspecies, the number of calls varied with time of day; Antarctic blue whale calls were more prevalent in the night to early morning, while Australian blue whale calls were detected more often from midday to early evening. Using passive acoustic monitoring, we show that each subspecies adopts different seasonal and daily call patterns which may be related to the ecological strategies of these subspecies. This study demonstrates the importance of passive acoustics in enabling us to understand and monitor subtle differences in the behavior and ecology of cryptic sympatric marine mammals

Blue whale songs worldwide: an update

Blue whales produce regionally-distinct songs. In over a decade since McDonald and colleagues published a summary of biogeographic differences in blue whale songs worldwide, multiple new publications have explored the seasonality and distribution of those songs. We review the spatial and temporal occurrence of previously-defined song types and report several new blue whale song types. At least thirteen songs believed to be produced by blue whales are now known worldwide, five more than reported in the previous review. In the North Pacific Ocean there are three blue whale songs: the well-studied Northeast Pacific song, the Central North Pacific (previously called Northwest and North Pacific) song, and a new song recorded off Hokkaido, Japan. There is spatial overlap of the Northeast Pacific and Central North Pacific songs in the Gulf of Alaska. Similarly, the new song co-occurs with the Central North Pacific song off Hokkaido. Only one blue whale song occurs in the North Atlantic. At least nine songs are present in the Southern Hemisphere. The Antarctic blue whale song is the most widely distributed, occurring in the Southern Ocean as well as seasonally extending into the other oceans of the Southern Hemisphere. The Indian Ocean has the largest variety of blue whale songs, with new data suggesting the Southwest Indian Ocean song should have type locality Madagascar, with Diego Garcia possibly another song-type. Southeast Pacific contains two distinct, co-occurring songs. We report a new song in the South Atlantic, near South Georgia Island, that also occurs seasonally off Ascension Island. Occasionally blue whale songs were recorded outside of their reported range, indicating individuals at times roam more broadly. However, this is not a common occurrence. This new information and finer details of occurrence will enable further development of hypotheses for blue whale population structure based on acoustics