Pheno- and genotypic characterization and identification of novel subtypes of Peste des Petits Ruminants virus in domestic and captive wild goats in Northern Iraq

Background Peste des Petits Ruminants (PPR) is an acute or peracute contagious transboundary viral disease that mainly affects caprine and ovine and causes significant economic impact in developing countries. After two PPR virus outbreaks in 2011 and 2014, an investigation, from August 2015 to September 2016, was carried out in Northern Iraq when an increased morbidity and mortality rates were reported in the domestic and captive wild goats. In the present study, ten domestic goat farms and seven captive wild goat herds located in seven geographical areas of Northern Iraq were clinically, pathologically, serologically and genotypically characterized to determine the prevalence and potential cause of PPR virus outbreak. Results The outbreak occurred with rate of morbidity (26.1%) and mortality (11.1%) in domestic goat farms as compared to captive wild goat herds where relatively high mortality (42.9%) and low morbidity (10.9%) rates were recorded. Based on the clinical symptoms (mucopurulent nasal discharges, ulceration and erosion of oral mucosa, profuse watery diarrhea) and necropsy (hemorrhage and congestion on mucous membranes of the colon and rectum with zebra stripes lesions) results, overall, the serological test findings revealed a high frequency (47.9%) of positive samples for anti-PPRV nucleoprotein antibodies. Furthermore, the nucleoprotein (N) gene was detected in 63.2 and 89.1% of samples using conventional and reverse transcription real-time quantitative PCR assays. A phylogenetic analysis of N gene amino acid sequences clustered with the reference strain revealed lineage IV similar to the strains isolated in 2011 and 2014, respectively. However, two sub-types of lineage IV (I and II), significantly distinct from the previous strains, were also observed. Conclusion The phylogenetic analysis suggests that movements of goats are possible cause and one of the important factors responsible for the spread of virus across the region. The study results would help in improving farm management practices by establishing a PPR virus eradication program using regular monitoring and vaccination program to control and mitigate the risk of re-emergence of PPR virus infection in domestic and captive wild goats in Iraq.

Analysis and Sequence Alignment of Peste des Petits Ruminants Virus ChinaSX2020

The peste des petits ruminants virus (PPRV) mainly infects goats and sheep and causes a highly contagious disease, PPR. Recently, a PPRV strain named ChinaSX2020 was isolated and confirmed following an indirect immunofluorescence assay and PCR using PPRV-specific antibody and primers, respectively. A sequencing of the ChinaSX2020 strain showed a genome length of 15,954 nucleotides. A phylogenetic tree analysis showed that the ChinaSX2020 genome was classified into lineage IV of the PRRV genotypes. The genome of the ChinaSX2020 strain was found to be closely related to PPRVs isolated in China between 2013 and 2014. These findings revealed that not a variety of PRRVs but similar PPRVs were continuously spreading and causing sporadic outbreaks in China.

Epidemiology and molecular characterization of re-emerged virulent strains of Peste des Petits Ruminants virus among sheep in Kassala State, Eastern Sudan

Background Peste des Petits Ruminants (PPR) is a severe contagious viral disease, which mainly affects small ruminants. PPR is caused by a Morbillivirus that belongs to the family Paramyxoviridae. In this study 12 suspected PPR outbreaks among sheep and goats were investigated in four localities in Kassala State, Eastern Sudan, during 2015—2017. The causative agent was confirmed by a Sandwich Enzyme-Linked Immunosorbent Assay (sELISA), and a Reverse Transcription Polymerase Chain Reaction (RT-PCR) targeting a partial sequence of nucleocapsid protein gene (N- gene) and a partial sequence of fusion protein gene (F- gene). Sequencing and phylogenetic analysis were carried out on six N- gene based RT-PCR products selected from two outbreaks occurred on border and inner localities of Kassala State to determine the circulating lineages of PPRV strains. Identity percentages were determined between isolates in this study and previous Sudanese, and other (African and Asian) isolates which clustered along with them. Results Out of 30 samples, 22 (73.3%) were positive using sandwich ELISA. From 22 s ELISA positive samples, 17 (77.3%) were positive by Ngene based RT-PCR and only 7(43.8%) out of 16 positive samples by N gene based RT-PCR were positive using Fgene based RT-PCR. The sequencing and phylogenetic analysis confirmed involvement of the lineage IV of PPRV in outbreaks among small ruminants in Kassala State and high identity percentage between our isolates and previous Sudanese and other (African and Asian) isolates. Conclusions The present study demonstrates that genetic relationship between PPRV strains circulating in sheep in Kassala State, Eastern Sudan, and PPRV strains characterized as lineage IV in neighboring African countries such as Eretria,Ethiopia, Egypt, and other Asian countries

Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India

From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of individuals from 17 states/Union Territories of the country who had received two doses (n = 592) and one dose (n = 85) of vaccines and tested positive for COVID-19. These cases were telephonically interviewed and clinical data were analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both groups. Analysis of both groups determined that 86.69% (n = 443) of them belonged to the Delta variant, along with Alpha, Kappa, Delta AY.1, and Delta AY.2. The Delta variant clustered into four distinct sub-lineages. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. This study indicates that majority of the breakthrough COVID-19 clinical cases were infected with the Delta variant, and only 9.8% cases required hospitalization, while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.

Clinical characterization and Genomic analysis of COVID-19 breakthrough infections during second wave in different states of India

During March to June 2021 India has experienced a deadly second wave of COVID19 with an increased number of post vaccination breakthrough infections reported across the country. To understand the possible reason of these breakthroughs we collected 677 clinical samples (throat swab/ nasal swabs) of individuals who had received two doses (n=592) and one dose (n=85) of vaccines (Covishield and Covaxin,) and tested positive for COVID19, from 17 states/Union Territories of country. These cases were telephonically interviewed and clinical data was analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both the cases. Analysis of both the cases determined that 86.69% (n=443) of them belonged to the Delta variant along with Alpha, Kappa, Delta AY.1 and Delta AY.2. The Delta variant clustered into 4 distinct sub-lineages. Sub-lineage I had mutations: ORF1ab, A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, A6319V and N G215C; Sub lineage II : ORF1ab P309, A3209V, V3718A, G5063S, P5401L and ORF7a L116F; Sub lineage III : ORF1ab A3209V, V3718A, T3750I, G5063S, P5401L and Spike A222V; Sub-lineage IV ORF1ab P309L, D2980N, F3138S and spike K77T. This study indicated that majority of the clinical cases in the breakthrough were infected with the Delta variant and only 9.8% cases required hospitalization while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.

Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification

Columnea latent viroid (CLVd) is a member of the Pospiviroid family and its naked circular RNA genome typically forms native “rod-like” secondary structures. In this work, the CLVd taxonomy was reevaluated based on sequence similarity and phylogenetic analysis, as well as the evaluation of the symptom development and disease severity of four selected CLVd isolates in a range of host species. The phylogenetic analysis showed that all CLVd isolates were clustered into five distinct clades: (I) severe isolates originally found in tomato crops in Thailand, (II) ornamental isolates, (III) mild isolates originally found in tomato crops in Thailand, and two clades (IV and V) containing mild isolates originating mainly from tomato crops in European countries, with different virulence levels on several hosts. Our analysis demonstrated that some CLVd isolates have a sequence similarity of less than 90% within the species taxon, as well as distinct biological characteristics (symptom development and virulence), both of which are important ICTV criteria for viroid classification. For these reasons, we propose that CLVd should be re-classified into at least three main taxonomic lineages: a “CLVd-tomato Asian lineage” (I), a “CLVd-tomato European lineage” (IV) and a “CLVd-ornamental European lineage” (II), plus two minor lineages (III and V), fitting the ICTV criteria.

Understanding the factors that determine the emergence of anthroponotic cutaneous leishmaniasis due to Leishmania tropica: Comparison of the density and mitochondrial lineage of Phlebotomus sergenti between endemic and free areas in Morocco

Anthroponotic cutaneous leishmaniasis (ACL) due to Leishmania tropica is spreading to new areas. Exposure to the vector, Phlebotomus sergenti, is the only proven risk factor. Our objective was to compare the densities and genetic characteristics of P. sergenti populations in two nearby localities in Morocco, one within an ACL endemic area (El Borouj) and another undamaged (Sidi Hajjaj). Statistically significant differences were detected between P. sergenti densities with a higher density of P. sergenti in the endemic town (p≤ 0.032). A different main P. sergenti mitochondrial lineage was evidenced in each one of the 2 localities, and for the first time, the lineage of P. sergenti specimens that are acting as a vector of L. tropica has been identified. Bioclimatic differences were detected between both localities. In conclusion, between an ACL endemic locality and another ACL free there are differences in both the density of P. sergenti and the mitochondrial lineage that may explain the different epidemiological situation. Given that the density of P. sergenti in the locality without ACL cases seems sufficient to allow transmission, the main factor that would justify its ACL undamaged character could be the absence of P. sergenti Lineage IV, which seems to prefer warmer and drier climates.

A Sequential Study on the Pathology of Peste Des Petits Ruminants and Tissue Distribution of the Virus Following Experimental Infection of Black Bengal Goats

We studied the sequential pathology of peste des petits ruminants (PPR) in Black Bengal goats and analyzed virus distribution in tissues and virus shedding following experimental infection with a Bangladeshi isolate of lineage IV PPR virus (PPRV). The early clinical signs like fever, depression, and ocular and nasal discharges first appeared at 4–7 days post-infection (dpi). Three out of eight inoculated goats died at 13, 15, and 18 dpi, and the rest were killed at different time points from 5 to 18 dpi. Initially, the virus multiplied mostly in the lymphoid organs of the pharyngeal region and caused extensive lymphoid destruction and hemorrhages. This was followed by viremia, massive virus replication in the lungs, and pneumonia along with the appearance of the clinical signs. Subsequently, the virus spread to other organs causing necrotic and hemorrhagic lesions, as well as the virus localized in the upper respiratory, oral and intestinal mucosa resulting in catarrhal, erosive, and ulcerative lesions. On hematological and biochemical investigation progressive leukopenia and hypoproteinemia, a gradual increase of serum metabolites and enzymes associated with liver and kidney damage, and electrolyte imbalance were observed. Seroconversion started at 7 dpi and all the surviving animals had serum antibodies at 14 dpi. Virus shedding was observed in nasal and ocular secretions at 4 dpi and in feces and urine at 14 dpi, which gradually increased and continued till the end of the experiment (18 dpi) despite seroconversion. Therefore, the virus shedding of naturally infected seroconverted goats should be monitored for effective control strategies.

Lassa Virus Circulation in Small Mammal Populations in Bo District, Sierra Leone

Lassa fever is a viral hemorrhagic fever caused by the Lassa virus LASV, which was first isolated in the rodent Mastomys natalensis in 1974 in Kenema, Sierra Leone. As little is known about the abundance and the presence of LASV in rodents living in the Bo area, we carried out a small mammal longitudinal population survey. A standardized trapping session was performed in various habitats and seasons in six villages over two years (2014–2016) and samples collected were tested for arenavirus IgG and LASV. A Bayesian phylogenetic analysis was performed on sequences identified by PCR. A total of 1490 small mammals were collected, and 16 rodent species were identified, with M. natalensis (355, 24%) found to be the most prevalent species. Forty-one (2.8%) samples were IgG positive, and 31 of these were trapped in homes and 10 in surrounding vegetation. Twenty-nine of 41 seropositive rodents were M. natalensis. We detected four LASV by PCR in two villages, all found in M. natalensis. Phylogenetic analysis showed that the sequences were distributed within the Sierra Leonean clade within lineage IV, distinguishing a Bo sub-clade older than a Kenema sub-clade. Compared to other settings, we found a low abundance of M. natalensis and a low circulation of LASV in rodents in villages around Bo district.

Molecular Epidemiology of Peste Des Petits Ruminants Cases Associated with Abortion in Sheep and Goat in Marmara Region of Turkey, 2018

The aim of this study was to investigate the molecular epidemiology of peste des petits ruminants (PPR) infections associated with abortion in sheep and goat samples from the Marmara region of Turkey during 2018. The study was carried out from 116 sheep and 26 goat abortion cases. PPR virus (PPRV) detection in these samples was performed using real-time RT-PCR (Q-RT-PCR). Then, sequence analysis was performed from PPRV positive samples. Q-RT-PCR results demonstrated that 12 (10.34%) out of 116 sheep abortion samples and 3 (11.53%) out of 26 goat abortion samples were positive for PPRV genome. The sequence results of RT-PCR positive products revealed that the viruses causing the cases belong to lineage IV. Furthermore, molecular analysis showed that present cases were not related to PPRV vaccine strains or its mutants. Marmara region, where this study was conducted, is a neighbour of European countries such as Bulgaria and Greece. The first PPR cases in Europe were reported from Bulgaria at the beginning of 2018 and subsequently, other cases also reported before are mentioned in the present study. This study provides valuable information to understand the epidemiology of recently emerged PPRV cases in Europe and Turkey. Furthermore, because of the prevalence of PPRV in abortion samples in this study, these results suggest that PPRV may be one of the possible etiologic agents of abortions in sheep and goat. However, for clarification of the relationship between abortion and PPRV, there is need more robust epidemiological data and experimental infection studies