Next-generation sequencing of southern African Crimean-Congo haemorrhagic fever virus isolates reveals a high frequency of M segment reassortment

Crimean Congo haemorrhagic fever virus (CCHFV) is a bunyavirus with a single-stranded RNA genome consisting of three segments (S, M, L), coding for the nucleocapsid protein, envelope glycoproteins and RNA polymerase, respectively. To date only five complete genome sequences are available from southern African isolates. Complete genome sequences were generated for 10 southern African CCHFV isolates using next-generation sequencing techniques. The maximum-likelihood method was used to generate tree topologies for 15 southern African plus 26 geographically distinct complete sequences from GenBank. M segment reassortment was identified in 10/15 southern African isolates by incongruencies in grouping compared to the S and L segments. These reassortant M segments cluster with isolates from Asia/Middle East, while the S and L segments cluster with strains from South/West Africa. The CCHFV M segment shows a high level of genetic diversity, while the S and L segments appear to co-evolve. The reason for the high frequency of M segment reassortment is not known. It has previously been suggested that M segment reassortment results in a virus with high fitness but a clear role in increased pathogenicity has yet to be shown.The National Health Laboratory Service Research Trust, the Polio Research Foundation, South Africa, and University of the Free State Cluster funding.http://journals.cambridge.org/action/displayJournal?jid=HYG2015-05-30am201

Comparative analysis of the L, M, and S RNA segments of Crimean-Congo haemorrhagic fever virus isolates from southern Africa

Crimean–Congo haemorrhagic fever virus (CCHFV) is a member of the Bunyaviridae family with a tripartite, negative sense RNA genome. This study used predictive software to analyse the L (large), M (medium), and S (small) segments of 14 southern African CCHFV isolates. The OTU-like cysteine protease domain and the RdRp domain of the L segment are highly conserved among southern African CCHFV isolates. The M segment encodes the structural glycoproteins, GN and GC, and the non-structural glycoproteins which are post-translationally cleaved at highly conserved furin and subtilase SKI-1 cleavage sites. All of the sites previously identified were shown to be conserved among southern African CCHFV isolates. The heavily O-glycosylated N-terminal variable mucin-like domain of the M segment shows the highest sequence variability of the CCHFV proteins. Five transmembrane domains are predicted in the M segment polyprotein resulting in three regions internal to and three regions external to the membrane across the GN, NSM and GC glycoproteins. The corroboration of conserved genome domains and sequence identity among geographically diverse isolates may assist in the identification of protein function and pathogenic mechanisms, as well as the identification of potential targets for antiviral therapy and vaccine design. As detailed functional studies are lacking for many of the CCHFV proteins, identification of functional domains by prediction of protein structure, and identification of amino acid level similarity to functionally characterised proteins of related viruses or viruses with similar pathogenic mechanisms are a necessary step for selection of areas for further study.National Health Laboratory Service Research Trust, the Polio Research Foundation, South Africa and University of the Free State Cluster funding.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1096-90712016-05-31hb201

Risk profiles and one-year outcomes of patients with newly diagnosed atrial fibrillation in India: Insights from the GARFIELD-AF Registry.

BACKGROUND: The Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF) is an ongoing prospective noninterventional registry, which is providing important information on the baseline characteristics, treatment patterns, and 1-year outcomes in patients with newly diagnosed non-valvular atrial fibrillation (NVAF). This report describes data from Indian patients recruited in this registry. METHODS AND RESULTS: A total of 52,014 patients with newly diagnosed AF were enrolled globally; of these, 1388 patients were recruited from 26 sites within India (2012-2016). In India, the mean age was 65.8 years at diagnosis of NVAF. Hypertension was the most prevalent risk factor for AF, present in 68.5% of patients from India and in 76.3% of patients globally (P < 0.001). Diabetes and coronary artery disease (CAD) were prevalent in 36.2% and 28.1% of patients as compared with global prevalence of 22.2% and 21.6%, respectively (P < 0.001 for both). Antiplatelet therapy was the most common antithrombotic treatment in India. With increasing stroke risk, however, patients were more likely to receive oral anticoagulant therapy [mainly vitamin K antagonist (VKA)], but average international normalized ratio (INR) was lower among Indian patients [median INR value 1.6 (interquartile range {IQR}: 1.3-2.3) versus 2.3 (IQR 1.8-2.8) (P < 0.001)]. Compared with other countries, patients from India had markedly higher rates of all-cause mortality [7.68 per 100 person-years (95% confidence interval 6.32-9.35) vs 4.34 (4.16-4.53), P < 0.0001], while rates of stroke/systemic embolism and major bleeding were lower after 1 year of follow-up. CONCLUSION: Compared to previously published registries from India, the GARFIELD-AF registry describes clinical profiles and outcomes in Indian patients with AF of a different etiology. The registry data show that compared to the rest of the world, Indian AF patients are younger in age and have more diabetes and CAD. Patients with a higher stroke risk are more likely to receive anticoagulation therapy with VKA but are underdosed compared with the global average in the GARFIELD-AF. CLINICAL TRIAL REGISTRATION-URL: http://www.clinicaltrials.gov. Unique identifier: NCT01090362

Juvenile survival and population regulation in southern elephant seals at Marion Island

We examined annual juvenile survival in southern elephant seals (Mirounga leonina) at Marion Island for the period 1994–1999 during which time the population was stable. Using mark–recapture models, we tested for age- and sex-specific differences in survival rates over the first three years of life. We found that survival was age- but not sex-related and compared our estimates to similar estimates from a previous study on the same population while in a state of decline. This was done to determine whether changes in juvenile survival were instrumental in terminating the population decline at Marion Island. On average, the probability of survival was 59.5 %, 81.4 % and 78.1 % for the first, second and third year respectively. These estimates were remarkably similar to those previously calculated for the population while in a state of decline, and we dismiss juvenile survival as a major population regulating component in southern elephant seals at Marion Island.Keywords: southern elephant seals, juvenile survival, mark–recapture, population regulation

Dispersion of a southern elephant seal Mirounga leonina to Possession Island, Namibia

Whilst southern elephant seals Mirounga leonina inhabit the Southern Ocean, hauling out on sub-Antarctic islands, individuals are frequently encountered further north, on southern hemisphere continents. It is unknown whether these animals are merely vagrants or whether they are individuals using the extremes of their range. A single adult male, identified by characteristic scars, was sighted 37 times from 2008 to 2021 at Possession Island, Namibia. The timing of sightings indicates that this individual must have remained in African waters between at least some of its haul-outs, rather than returning to the Southern Ocean. Similar observations have been reported anecdotally for other individual adult male elephant seals on the southern African coast, whilst adult females pupping in this area are extremely rare. Although records of vagrant southern elephant seals hauling out on the southern African coast remain rare, whether they are single or repeated visits, in some instances repeated haul-outs represent dispersion to rewarding foraging areas.https://link.springer.com/journal/3002023-03-16hj2023Mammal Research InstituteZoology and Entomolog

Killer whales (Orcinus orca) at Marion Island, Southern Ocean

Killer whales (Orcinus orca) were studied using data obtained on an opportunistic basis between 1973 and 1996 at Marion Island (46°54’S, 37°45’E) in the Southern Indian Ocean. A clear seasonal pattern of occurrence with the main peak between October and December was evident. Most killer whales were observed within 5 m of the shore and adult males typically occurred further offshore than adult females. The distribution of killer whales around the island was not uniform and more than 80 % of all sightings occurred close to the base station. This was probably due to a  concentration of search effort in the vicinity of the base station and to an uneven distribution of prey species. Killer whales occurred in groups with an average of 3.56 individuals and a maximum of 28 animals per group; females predominated throughout the study. Dawn-to-dusk surveys of killer whales in the near-shore waters during 1986, 1989 and 1990 showed small, statistically non-significant peaks of sightings in the early morning and late afternoon. Twenty-six killer whales were individually identified from photographs, eleven of which recurred at Marion Island. Modified photogrammetric methods may improve current photogrammetric analysis of cetacean dorsal fins.Key words: population structure; seasonal patterns, photogrammetry

Evidence for density dependent population regulation in southern elephant seals in the southern Indian Ocean

The means by which populations are regulated form a central theme in conservation biology, and much debate has revolved around density dependence as a mechanism driving population change. Marion Island (46°54’S, 37°45’E) is host to a relatively small breeding population of southern elephant seals, which like its counterparts in the southern Indian and southern Pacific Oceans, have declined precipitously over the past few decades. An intensive mark– recapture study, which commenced in 1983, has yielded a long time-series of resight data on this population. We used the program MARK to estimate adult female survival in this population from resight data collected over the period 1986–1999. Including concurrent population counts as covariates significantly improved our mark–recapture models and suggests density dependent population regulation to be operational in the population. Although  predation may have been involved, it is far more likely that density dependent regulation has been based on a limited food supply. A significant increase in adult female survival was evident which is likely to have given rise to recent  changes in population growth.Key words: density dependence, southern elephant seals, Marion Island, population regulation

Pup growth and maternal attendance patterns in Subantarctic fur seals

Samples of pups from the expanding populations of Subantarctic fur seals  (Arctocephalus tropicalis) at Marion and Gough islands were weighed at specific ages between birth and weaning in the period 1993-2000. Growth was estimated and compared between years, sexes, sites of different density, and populations. Pups of comparable age were consistently heavier at Marion Island than at Gough Island, probably reflecting relative prey resource abundance. No changes in pup growth rates were apparent over the study period, nor was there any evidence that growth was affected by ENSO events. Measures of pup growth at Marion Island were complemented by measures of maternal attendance behaviour during three summer and winter  seasons. More years of data are required to determine patterns between attendance, growth, resource conditions and population abundance trends.Key words: Subantarctic fur seal, Marion Island, Gough Island, pup growth, maternal attendance behaviour