Empirical Bayes estimation of farm prevalence adjusting for multistage sampling and uncertainty in test performance: a Brucella cross-sectional serostudy in southern Kazakhstan.

Estimation of farm prevalence is common in veterinary research. Typically, not all animals within the farm are sampled, and imperfect tests are used. Often, assumptions about herd sizes and sampling proportions are made, which may be invalid in smallholder settings. We propose an alternative method for estimating farm prevalence in the context of Brucella seroprevalence estimation in an endemic region of Kazakhstan. We collected 210 milk samples from Otar district, with a population of about 1000 cattle and 16 000 small ruminants, and tested them using an indirect ELISA. Individual-level prevalence and 95% confidence intervals were estimated using Taylor series linearization. A model was developed to estimate the smallholding prevalence, taking into account variable sampling proportions and uncertainty in the test accuracy. We estimate that 73% of households that we sampled had at least one Brucella-seropositive animal (95% credible interval 68-82). We estimate that 58% (95% confidence interval 40-76) of lactating small ruminants and 14% (95% confidence interval 1-28) of lactating cows were seropositive. Our results suggest that brucellosis is highly endemic in the area and conflict with those of the official brucellosis-testing programme, which found that in 2013 0% of cows and 1·7% of small ruminants were seropositive.

Comparative evaluation of effectiveness of IAVchip DNA microarray in influenza A diagnosis.

The paper describes comparative evaluation of IAVchip DNA microarray, reverse transcription PCR (RT-PCR), and real-time RT-PCR versus virus isolation in chicken embryos and shows their diagnostic effectiveness in detection and subtyping of influenza A virus. The tests were evaluated with use of 185 specimens from humans, animals, and birds. IAVchip DNA microarray demonstrates higher diagnostic effectiveness (99.45%) in early influenza A diagnosis as compared to the real-time PCR (98.38%) and RT-PCR (96.22%), thus showing its clear superiority. Diagnostic sensitivity of IAVchip DNA microarray (100%) exceeds the same of RT-PCR (95.95%) and real-time RT-PCR (97.96%) in the range of estimated confidence intervals. IAVchip DNA microarray and real-time RT-PCR displayed equal diagnostic specificity (98.85%), while diagnostic specificity of RT-PCR was 96.40%. IAVchip DNA microarray has an advantage over the other tests for influenza A diagnosis and virus identification as a more rapid method that allows performing simultaneous detection and subtyping of about tens of specimens within one experiment during 8-10 hours. The developed IAVchip DNA microarray is a general test tool that enables identifying simultaneously 16 hemagglutinin (HA) and 9 neuraminidase (NA) subtypes of influenza A virus and also to screen the influenza A viruses from humans, animals, and birds by M and NP genes.

Goatpox virus (G20-LKV) vaccine strain elicits a protective response in cattle against lumpy skin disease at challenge with lumpy skin disease virulent field strain in a comparative study.

In this comparative study, we examine the safety of the sheeppox (SPP) and goatpox (GTP) vaccines and the protective response of these vaccines in cattle against a virulent lumpy skin disease (LSD) field strain. The vaccine safety was tested in rabbits, mice and cattle using ten times recommended dose. In the safety trial, none of the vaccinated animals showed any deviation from physiological norms or fever, inappetence or local/ generalized skin reactions. In the challenge trial, both SPP and GTP vaccine groups developed virus-neutralizing antibodies with an average titre of 2.1 log2 at 21 days post-vaccination. No significant difference in seroconversion was found in cattle vaccinated with SPP and GTP vaccines (P ≥ 0.05). When challenged with a virulent LSD field strain, one animal vaccinated with the SPP Niskhi vaccine strain showed typical LSD skin lesions at the injection sites of different dilutions of the challenge virus. All animals vaccinated with GTP G20-LKV vaccine strain showed full protection. After infection with the challenge virus, unvaccinated fully susceptible control cattle showed characteristic clinical signs of LSD. The average protective index for SPP and GTP vaccine groups was 5.3 ± 1.42 and 5.9 ± 0.00, respectively.

Genomic Sequence of the New Attenuated Vaccine Strain Neethling-RIBSP of the Lumpy Skin Disease Virus.

We report here the draft genome sequence of the new attenuated strain Neethling-RIBSP of the lumpy skin disease virus, obtained by sequential and alternating passages in cell culture and developing chicken embryos. Genome sequencing allowed the identification of differentiation markers of the new strain.

Detection and Genetic Characterization of Lineage IV Peste Des Petits Ruminant Virus in Kazakhstan.

Peste des petits ruminant (PPR) is endemic in many Asian countries with expansion of the range in recent years including across China during 2013-2014 (OIE, 2014). Till the end of 2014, no cases of PPR virus (PPRV) were officially reported to the Office Internationale des Epizooties (OIE) from Kazakhstan. This study describes for the first time clinicopathological, epidemiological and genetic characterization of PPRV in 3 farm level outbreaks reported for the first time in Zhambyl region (oblast), southern Kazakhstan. Phylogenetic analysis based on partial N gene sequence data confirms the lineage IV PPRV circulation, similar to the virus that recently circulated in China. The isolated viruses are 99.5-99.7% identical to the PPRV isolated in 2014 from Heilongjiang Province in China and therefore providing evidence of transboundary spread of PPRV. There is a risk of further maintenance of virus in young stock despite vaccination of adult sheep and goats, along livestock trade and pastoral routes, threatening both small livestock and endangered susceptible wildlife populations throughout Kazakhstan.

Comparison of influenza outbreaks in the Republic of Kazakhstan and Russia induced by 2009 yearly new variant of A(H1N1) influenza virus.

The aim of the work is the comparison of the epidemiology of influenza and acute respiratory virus infections (ARVI) in the Republic of Kazakhstan with the corresponding influenza epidemic in Russia induced by influenza pandemic virus A/California/07/2009 in 2009. Data on influenza and ARVI from the Republic of Kazakhstan and Federal Center of influenza was collected and investigated over the course of several weeks from hospitalized patients with the same diagnosis among all population and in age groups on 16 territories of Kazakhstan and in 49 major cities of Russia. The epidemic in Kazakhstan resembled the Russian epidemic in terms of its abnormally early beginning, expression of monoaetiology, the spread of the epidemic into all territories and start of the epidemics among adult population. High percentage of hospitalized people and lethal outcome were registered in this epidemic. Similarity of epidemic process character in corresponding border-line territories of both countries was found out.