Molecular Characterization of Circulating DENV-2 During Outbreak in Northern Senegal, Rosso 2018

Globally 390 millions of people are at risk of dengue infection; over the past 50 years the virus incidence increased thirty-fold. In Senegal, an unprecedented occurrence of outbreaks and sporadic cases was noticed since 2017. In October 2018 an outbreak of DENV-2 was reported in Rosso area in the north of Senegal at the border with Mauritania. Out of the 187 blood specimen samples collected, 27 were positives by qRT-PCR and 8 were serologically positive for DENV IgM. Serotyping using qRT-PCR reveals that isolates were positive for DENV-2. A subset of DENV-2 positives samples was selected and subjected to full genome sequencing followed by phylogenetic analysis. Analysis of 06 nearly completed genome sequences (n= 6) revealed that isolates belong to the cosmopolitan genotype and are closely related to the Mauritanian strains detected between 2017 and 2018 and those detected in many West African countries such as Burkina Faso or Cote d’Ivoire. Our results suggest a transboundary circulation of the DENV-2 cosmopolitan genotype between Senegal and Mauritania and call for a need of coordinated surveillance of arboviruses between these two countries. Interestingly, high level of homology between West African isolates highlights endemicity and call for a set-up of sub-regional viral genomic surveillance which will lead to a better understanding of viral dynamic, transmission and spread across Africa.

Newspapers’ coverage of the COVID-19 pandemic in Eswatini: from distanciated re/presentations to socio-health panics

This paper examines the coverage and re/presentation of the coronavirus pandemic by two mainstream newspapers in the Kingdom of Eswatini, namely, the Times of Eswatini and the Eswatini Observer between January and June 2020. Framing and discourse analyses are used in the examination of news stories. The key to this study is how the coverage and re/presentation evolved as ‘new facts’ about the virus emerged. From being re/presented in a distanciated form to becoming a localised scare, the travelling of the virus in space and time and its profile in the newspapers are examined. When the virus began to enjoy widespread coverage, news stories focused on virus incidence and later started paying attention to the internal evolution of the virus and how the government was responding to it. The analysis shows that political indexing sustained the coverage of the COVID-19 pandemic. Due to political and official indexing, media coverage largely reproduced the views of those in power, especially the construction of lockdown regulations as rational and legitimate. The government and security officials characterised the coronavirus as an invading enemy that could only be defeated through ‘war’. The news media reproduced the war language of the government and security officials, and thus legitimised the lockdowns and security surveillance. In addition to regulatory interventions, the results reveal that the government and civil society initiated prayer and fasting sessions as part of response interventions. This paper concludes that health journalism pays less attention to health scares that are seen to be happening ‘elsewhere’. However, once the problems become local, the news value of proximity enables journalists to provide extensive coverage. In addition, the coverage of pandemics begins with increased coverage and panic, followed by constant attention and after some time, the stories leave front pages as journalism fatigue kicks in.

Cucurbit aphid-borne yellows virus (CABYV) infecting melon and bitter gourd in Java, Indonesia

Recently, Cucurbit aphid-borne yellows polerovirus (CABYV) had been reported firstly to infect cucumber in Java. The typical symptoms of CABYV infection are leaf yellowing with green veins and the thickening of older leaves. This study aimed to detect and identify the occurrence of CABYV infection on other cucurbit hosts in Java. A total of 600 Polerovirus-like symptomatic leaves were taken from open-fields cultivated plants in West Java, Central Java, and East Java. The virus incidence was determined serologically, RT-PCR and DNA sequencing confirmed the identity of CABYV. Based on serological test revealed six virus species in single or multiple infections with varying incidence. Among tested plants, the CABYV DNA with size ± 489 bp was successfully amplified from melon in Kediri, Tulungagung, Nganjuk (East Java), Kulonprogo, and bitter gourd in Bogor. The sequencing result confirmed the identity of melon isolates from Nganjuk showed the highest similarity with the CABYV cucumber isolate from Nganjuk and Tulungagung. In contrast, bitter gourd isolates with melon isolates from France and squash isolates from Spain. These are the first reports of CABYV infection on melon and bitter gourd in Java, indicating its rapid host expansion on Cucurbitaceae.

An integrated strategy for managing Grapevine leafroll-associated virus 3 in red berry cultivars in New Zealand vineyards

<p>To sustain growth and revenue projections, the New Zealand wine sector aims to produce premium quality wine to supply lucrative export markets. In grapevines, however, the presence of virus and virus-like diseases can negatively influence qualitative parameters of wine production. Where such risks are identified, sustainable remediation protocols should be developed. One risk factor is Grapevine leafroll-associated virus 3 (GLRaV-3), an economically important virus of Vitis. In this thesis, I develop components of an integrated management plan with the aim of reducing and sustaining GLRaV-3 incidence at <1%. In Hawke’s Bay vineyard study blocks, three aspects related to GLRaV-3 management were explored between 2008 and 2013: Firstly, herbicide-treated vines and/or land left fallow after removing infected vines may mitigate the effects of GLRaV-3. Historically though, vine root removal was not well implemented, meaning persistent roots may be long term reservoirs for GLRaV-3. I tested the virus reservoir hypothesis in vineyard blocks where virus incidence of ≥95% necessitated removing all vines. Enzyme-linked immunosorbent assay (ELISA) and/or real-time polymerase chain reaction (real-time PCR) detected GLRaV-3 in most remnant root samples tested, independent of the herbicide active ingredient applied (glyphosate, triclopyr, or metsulfuron) or the fallow duration (6 months to 4 years). On some virus-positive root samples, the GLRaV-3 mealybug vector, Pseudococcus calceolariae, was found, and after real-time PCR testing, virus was detected in some mealybugs. Thus, without effective vine removal, unmanaged sources of virus inoculum and viruliferous vectors could pose a risk to the health of replacement vines. Secondly, in most red berry cultivars, GLRaV-3 is characterised by dark red downward curling leaves with green veins. With visual diagnostics predicted to be a reliable identifier of GLRaV-3-symptomatic red berry vines, early identification could support a cost-effective and sustainable virus management plan. In blocks planted in Merlot, Cabernet Sauvignon, Syrah, and Malbec vines, the reliability of visual symptom identification was compared with ELISA. In terms of sensitivity (binomial generalised linear model, 0.966) and specificity (0.998), late-season visual diagnostics reliably predicted virus infection. Moreover, accuracy appeared unaffected by the genetically divergent GLRaV-3 populations detected in Hawke’s Bay. Thirdly, by acting to visually identify and remove (rogue) symptomatic vines when GLRaV-3 incidence is low (<20%), an epidemic may be averted. In this ongoing study, an integrated approach to virus management was adopted in 13 well established Hawke’s Bay vineyard study blocks. All were planted in vines from one of five red berry cultivars. When monitoring commenced in 2009, all symptomatic vines visually identified (n=2,544 or 12%) were rogued. Thereafter, integrating visual diagnostics with roguing reduced virus incidence so that by 2013, just 434 (2.0%) vines were identified with virus symptoms. Annual monitoring revealed within-row vines immediately either side of an infected vine were most at risk of vector mediated virus transmission, although by 2013, just 4% of these vines had virus symptoms. Hence, roguing symptomatic vines only was recommended. In individual study blocks in 2013, virus management was tracking positively in four blocks; while in another four, results were inconclusive. In the remaining five blocks, contrasting but definitive results were evident. In three of those blocks, mean virus incidence of 10% in 2009 was sustained at ≤0.3% within 2-3 years of roguing commencing; in the other two blocks, mean incidence was 12% but cumulative vine losses of 37% (2011) and 46% (2013) culminated in roguing being replaced with whole block removal. In all five blocks, roguing protocols were standardised but in those with effective virus control, mealybug numbers were significantly lower in all years (mean: <0.2 per vine leaf; p≤0.036) relative to those where all vines were removed (mean: 0.4-2.3 per vine leaf). Overall, the results of this research suggest that rather than adopting a single management tactic in isolation, effective GLRaV-3 control instead requires an integrated plan to be implemented annually.</p>

An integrated strategy for managing Grapevine leafroll-associated virus 3 in red berry cultivars in New Zealand vineyards

<p>To sustain growth and revenue projections, the New Zealand wine sector aims to produce premium quality wine to supply lucrative export markets. In grapevines, however, the presence of virus and virus-like diseases can negatively influence qualitative parameters of wine production. Where such risks are identified, sustainable remediation protocols should be developed. One risk factor is Grapevine leafroll-associated virus 3 (GLRaV-3), an economically important virus of Vitis. In this thesis, I develop components of an integrated management plan with the aim of reducing and sustaining GLRaV-3 incidence at <1%. In Hawke’s Bay vineyard study blocks, three aspects related to GLRaV-3 management were explored between 2008 and 2013: Firstly, herbicide-treated vines and/or land left fallow after removing infected vines may mitigate the effects of GLRaV-3. Historically though, vine root removal was not well implemented, meaning persistent roots may be long term reservoirs for GLRaV-3. I tested the virus reservoir hypothesis in vineyard blocks where virus incidence of ≥95% necessitated removing all vines. Enzyme-linked immunosorbent assay (ELISA) and/or real-time polymerase chain reaction (real-time PCR) detected GLRaV-3 in most remnant root samples tested, independent of the herbicide active ingredient applied (glyphosate, triclopyr, or metsulfuron) or the fallow duration (6 months to 4 years). On some virus-positive root samples, the GLRaV-3 mealybug vector, Pseudococcus calceolariae, was found, and after real-time PCR testing, virus was detected in some mealybugs. Thus, without effective vine removal, unmanaged sources of virus inoculum and viruliferous vectors could pose a risk to the health of replacement vines. Secondly, in most red berry cultivars, GLRaV-3 is characterised by dark red downward curling leaves with green veins. With visual diagnostics predicted to be a reliable identifier of GLRaV-3-symptomatic red berry vines, early identification could support a cost-effective and sustainable virus management plan. In blocks planted in Merlot, Cabernet Sauvignon, Syrah, and Malbec vines, the reliability of visual symptom identification was compared with ELISA. In terms of sensitivity (binomial generalised linear model, 0.966) and specificity (0.998), late-season visual diagnostics reliably predicted virus infection. Moreover, accuracy appeared unaffected by the genetically divergent GLRaV-3 populations detected in Hawke’s Bay. Thirdly, by acting to visually identify and remove (rogue) symptomatic vines when GLRaV-3 incidence is low (<20%), an epidemic may be averted. In this ongoing study, an integrated approach to virus management was adopted in 13 well established Hawke’s Bay vineyard study blocks. All were planted in vines from one of five red berry cultivars. When monitoring commenced in 2009, all symptomatic vines visually identified (n=2,544 or 12%) were rogued. Thereafter, integrating visual diagnostics with roguing reduced virus incidence so that by 2013, just 434 (2.0%) vines were identified with virus symptoms. Annual monitoring revealed within-row vines immediately either side of an infected vine were most at risk of vector mediated virus transmission, although by 2013, just 4% of these vines had virus symptoms. Hence, roguing symptomatic vines only was recommended. In individual study blocks in 2013, virus management was tracking positively in four blocks; while in another four, results were inconclusive. In the remaining five blocks, contrasting but definitive results were evident. In three of those blocks, mean virus incidence of 10% in 2009 was sustained at ≤0.3% within 2-3 years of roguing commencing; in the other two blocks, mean incidence was 12% but cumulative vine losses of 37% (2011) and 46% (2013) culminated in roguing being replaced with whole block removal. In all five blocks, roguing protocols were standardised but in those with effective virus control, mealybug numbers were significantly lower in all years (mean: <0.2 per vine leaf; p≤0.036) relative to those where all vines were removed (mean: 0.4-2.3 per vine leaf). Overall, the results of this research suggest that rather than adopting a single management tactic in isolation, effective GLRaV-3 control instead requires an integrated plan to be implemented annually.</p>

Estimating the impact of non-pharmaceutical interventions against COVID-19 on mumps incidence in Sichuan, China

Background A series of social and public health measures have been implemented to contain coronavirus disease 2019 (COVID-19) in China. We examined the impact of non-pharmaceutical interventions against COVID-19 on mumps incidence as an agent to determine the potential reduction in other respiratory virus incidence. Methods We modelled mumps incidence per month in Sichuan using a seasonal autoregressive integrated moving average (ARIMA) model, based on the reported number of mumps cases per month from 2017 to 2020. Results The epidemic peak of mumps in 2020 is lower than in the preceding years. Whenever compared with the projected cases or the average from corresponding periods in the preceding years (2017–2019), the reported cases in 2020 markedly declined (P < 0.001). From January to December, the number of mumps cases was estimated to decrease by 36.3% (33.9–38.8%), 34.3% (31.1–37.8%), 68.9% (66.1–71.6%), 76.0% (73.9–77.9%), 67.0% (65.0–69.0%), 59.6% (57.6–61.6%), 61.1% (58.8–63.3%), 49.2% (46.4–52.1%), 24.4% (22.1–26.8%), 30.0% (27.5–32.6%), 42.1% (39.6–44.7%), 63.5% (61.2–65.8%), respectively. The total number of mumps cases in 2020 was estimated to decrease by 53.6% (52.9–54.3%). Conclusion Our study shows that non-pharmaceutical interventions against COVID-19 have had an effective impact on mumps incidence in Sichuan, China.

Prevalence and genetic diversity of viruses associated with rugose wood complex in Greek vineyards

Rugose wood is one of the most important disease syndromes of grapevine and it has been associated with at least three viruses: grapevine rupestris stem pitting associated virus (GRSPaV), grapevine virus A (GVA) and grapevine virus B (GVB). All three viruses show a worldwide distribution pattern, and their genetic composition has been the focus of extensive research over the past years. Despite their first record in Greece almost 20 years ago, there is a lack of knowledge on the distribution and genetic variability of their populations in Greek vineyards. In this context, we investigated the distribution of GRSPaV, GVA and GVB in rootstocks, self-rooted and grafted grapevine cultivars, originating from different geographic regions that are representing important viticultural areas of Greece. Three new RT-PCR assays were developed for the reliable detection of GRSPaV, GVA and GVB. Our results indicated that GVA is the most prevalent in Greek vineyards, followed by GRSPaV and GVB. However, virus incidence differed among self-rooted and grafted grapevine cultivars or rootstocks tested. Selected isolates from each virus were further molecularly characterized to determine their phylogenetic relationships. All three viruses exhibited high nucleotide diversity, which was depicted in the constructed phylogenetic trees. Isolates from Greece were placed in various phylogroups, reinforcing the scenario of multiple introductions of GVA, GVB and GRSPaV in Greece and highlighting the effect of different transmission modes in the evolutionary course of the three viruses.

Incidence, geographical distribution and genetic diversity of sugarcane striate virus in Saccharum species in China

A novel virus of the genus Mastrevirus, family Geminivirdae, was recently reported in sugarcane germplasm collections in Florida, Guadeloupe and Réunion, and was named sugarcane striate virus (SStrV). Although the full-length sequence of a SStrV isolate from China was obtained in 2015, the incidence, geographical distribution, and genetic diversity of this virus remained unclear. A single leaf sample from 2,368 sugarcane plants from main sugarcane producing regions of China and germplasm collections were tested for SStrV by polymerase chain reaction (PCR). Average virus incidence was 25.1% for field collected samples and SStrV was detected in most Saccharum species and two sugarcane-related species with the highest incidence in S. officinarum (44.1%) followed by Saccharum spp. local varieties (33.3%) grown for chewing cane for a long time. The virus incidence was much lower (6.8%) in modern commercial cultivars (Saccharum spp. hybrids). Phylogenetic trees based on full-length genomes of 157 SStrV isolates revealed that Chinese isolates comprised strains A and B, but not C and D that were reported in Florida, USA. SStrV strain A was the most prominent (98.7%) and widespread strain in China and was further divided into eight sub-groups. Almost half (45.6%) of the SStrV-positive samples from S. officinarum and Saccharum spp. local varieties were co-infected with sugarcane mosaic disease viruses or sugarcane yellow leaf virus. Interestingly, most of the plants infected by strain A of SStrV were asymptomatic. SStrV appears to be widespread in China, and its influence on chewing cane deserves further investigation.