Chikungunya outbreak in Bangladesh (2017): sociodemographic and clinical characteristics of patients from three hotspots

Background Chikungunya is a severely debilitating disease. Bangladesh witnessed one of the largest outbreaks in 2017. Here, we described the clinical profile of the chikungunya outbreak in Bangladesh and its heterogeneity across three hotspots. Methods This was a descriptive cross-sectional study of 432 individuals interviewed from the outpatient department of three study sites (Dhaka, Chittagong, and Sitakundu Upazilla of Bangladesh) after confirmation by the study physicians. Both laboratory-confirmed cases and probable cases were recruited between July and October 2017. Results Of all, 18% (79) were laboratory confirmed, and 353 82% (335) were probable cases. The male:female ratio was almost equal (1.09:1), and the predominant age group was 18–59 years. The mean age of the presentation was 36.07 ± 13.62 (SD) years. Fever and arthralgia were the most common presentations and were present in > 95% of cases. Other frequent symptoms were fatigue, myalgia, headache, nausea, and vomiting. Approximately half of the patients had arthritis and erythematous rash. Arthritis was predominant in Chittagong city, while maculopapular rash was not observed in Sitakunda city. However, fatigue, nausea, and vomiting are more common among patients in Dhaka city. Significant heterogeneity of clinical manifestations was present across the three hotspots (p < 0.05 for all). Both confirmed and probable cases shared similar characteristics except muscle ache (p = 0.22) and rash (p = 0.37). Conclusion The clinical profile of chikungunya virus-induced disease displays significant location-related heterogeneity in Bangladesh during a large outbreak. Although the causes of such differences are unclear, improved public and medical personnel education on this condition may lead to earlier diagnosis and treatment.

An Analysis of the Possible Migration Routes of Oedaleus decorus asiaticus Bey-Bienko (Orthoptera: Acrididae) from Mongolia to China

Oedaleus decorus asiaticus (Bey-Bienko) is a destructive pest in grasslands and adjacent farmland in northern China, Mongolia, and other countries in Asia. It has been supposed that this insect pest can migrate a long distance and then induce huge damages, however, the migration mechanism is still unrevealed. The current study uses insect light trap data from Yanqing (Beijing), together with regional meteorological data to determine how air flow contributes to the long-distance migration of O. decorus asiaticus. Our results indicate that sinking airflow is the main factor leading to the insects’ forced landing, and the prevailing northwest wind was associated with O. decorus asiaticus taking off in the northwest and moving southward with the airflow from July to September. Meanwhile, the insects have a strong migratory ability, flying along the airflow for several nights. Thus, when the airflow from the northwest met the northward-moving warm current from the southwest, a large number of insects were dropped due to sinking airflow, resulting in a large outbreak. Our simulations suggest that the source of the grasshoppers involved in these outbreaks during early 2000s in northern China probably is in Mongolia, and all evidence indicates that there are two important immigrant routes for O. decorus asiaticus migration from Mongolia to Beijing. These findings improves our understanding of the factors guiding O. decorus asiaticus migration, providing valuable information to reduce outbreaks in China that have origins from outside the country.

First Detection of Rotavirus C in Asymptomatic Pigs from India with Unexpected Dominance and Characterization of the Structural and Nonstructural Genes

Epidemiological and molecular investigation was conducted on Rotavirus C (RVC), the viral agent documented with rising prevalence rate, disease severity and cross species transmission and large outbreak potential. Fecal specimens of pigs collected from two cities of Maharashtra state, India tested for RVC showed 20.1% detection rate with majority below 3 months of age. No significant difference in detection rates was observed in the specimens collected in 2009 from Northern and in 2013 from Western parts of Maharashtra. The phylogenetic analyses showed presence of the I7 and I10 genotypes of the VP6 gene and representative strains with G1 and E5 genotypes of the VP7 and NSP4 gene respectively. Full genome characterization of a single strain showed presence of G1, P1, I7, R1, C1, M3, A1, N5, T5, E5, H1 genotypes of the VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5 genes respectively. This is the first evidence of detection of porcine RVC in asymptomatic pigs in India as well as with highest detection rate reported in asymptomatic pigs till date globally. Identification of porcine RVC at two time intervals and two different parts of Maharashtra state indicates the possibility of continuous circulation of RVC in pig population through asymptomatic infections.

Genetic diversity of Leptospira isolates in Lao PDR and genome analysis of an outbreak strain

Background Although Southeast Asia is one of the most leptospirosis afflicted regions, little is known about the diversity and molecular epidemiology of the causative agents of this widespread and emerging zoonotic disease. Methodology/Principal findings We used whole genome sequencing to examine genetic variation in 75 Leptospira strains isolated from patients in the Lao PDR (Laos) between 2006 and 2017. Eleven serogroups from 4 Leptospira species and 43 cgMLST-defined clonal groups (CGs) were identified. The most prevalent CG was CG272 (n = 18, 26.8%), composed of L. interrogans serogroup Autumnalis isolates. This genotype was recovered throughout the 12-year period and was associated with deaths, and with a large outbreak in neighbouring Thailand. Genome analysis reveals that the CG272 strains form a highly clonal group of strains that have, for yet unknown reasons, recently spread in Laos and Thailand. Additionally, accessory genes clearly discriminate CG272 strains from the other Leptospira strains. Conclusions/Significance The present study reveals a high diversity of Leptospira genotypes in Laos, thus extending our current knowledge of the pan- and core-genomes of these life-threatening pathogens. Our results demonstrate that the CG272 strains belong to a unique clonal group, which probably evolved through clonal expansion following niche adaptation. Additional epidemiological studies are required to better evaluate the spread of this genotype in Southeast Asia. To further investigate the key factors driving the virulence and spread of these pathogens, more intense genomic surveillance is needed, combining detailed clinical and epidemiological data.

How a school holiday led to persistent COVID-19 outbreaks in Europe

This paper investigates the role of large outbreaks on the persistence of Covid-19 over time. Using data from 650 European regions in 14 countries, I first show that winter school holidays in late February/early March 2020 (weeks 8, 9 and 10) led to large regional outbreaks of Covid-19 in the spring with the spread being 60% and up-to over 90% higher compared to regions with earlier school holidays. While the impact of these initial large outbreaks fades away over the summer months, it systematically reappears from the fall as regions with school holidays in weeks 8, 9 and 10 had 30–70% higher spread. This suggests that following a large outbreak, there is a strong element of underlying (latent) regional persistence of Covid-19. The strong degree of persistence highlights the long-term benefits of effective (initial) containment policies, as once a large outbreak has occurred, Covid-19 persists. This result emphasizes the need for vaccinations against Covid-19 in regions that have recently experienced large outbreaks but are well below herd-immunity, to avoid a new surge of cases.

Agritourism and Kidding Season: A Large Outbreak of Human Shiga Toxin-Producing Escherichia coli O157 (STEC O157) Infections Linked to a Goat Dairy Farm—Connecticut, 2016

The objective of this study was to determine sources of Shiga toxin-producing Escherichia coli O157 (STEC O157) infection among visitors to Farm X and develop public health recommendations. A case-control study was conducted. Case-patients were defined as the first ill child (aged &lt;18 years) in the household with laboratory-confirmed STEC O157, or physician-diagnosed hemolytic uremic syndrome with laboratory confirmation by serology, who visited Farm X in the 10 days prior to illness. Controls were selected from Farm X visitors aged &lt;18 years, without symptoms during the same time period as case-patients. Environment and animal fecal samples collected from Farm X were cultured; isolates from Farm X were compared with patient isolates using whole genome sequencing (WGS). Case-patients were more likely than controls to have sat on hay bales at the doe barn (adjusted odds ratio: 4.55; 95% confidence interval: 1.41–16.13). No handwashing stations were available; limited hand sanitizer was provided. Overall, 37% (29 of 78) of animal and environmental samples collected were positive for STEC; of these, 62% (18 of 29) yielded STEC O157 highly related by WGS to patient isolates. STEC O157 environmental contamination and fecal shedding by goats at Farm X was extensive. Farms should provide handwashing stations with soap, running water, and disposable towels. Access to animal areas, including animal pens and enclosures, should be limited for young children who are at risk for severe outcomes from STEC O157 infection. National recommendations should be adopted to reduce disease transmission.

Management of a large outbreak of COVID-19 at a British Army training centre: lessons for the future

IntroductionThe COVID-19 pandemic has posed major challenges for infection control within training centres, both civilian and military. Here we present a narrative review of an outbreak that occurred at the Royal Military Academy Sandhurst (RMAS) in January–March 2021, in the context of the circulating, highly transmissible SARS-CoV-2 variant B.1.1.7.MethodsTesting for SARS-CoV-2 was performed using a combination of reverse transcriptase PCR and Lateral Flow Devices (LFDs). Testing and isolation procedures were conducted in line with a pre-established symptom stratification system. Genomic sequencing was performed on 10 sample isolates.ResultsBy the end of the outbreak, 185 cases (153 Officer Cadets, 32 permanent staff) had contracted confirmed COVID-19. This represented 15% of the total RMAS population. This resulted in 0 deaths and 0 hospitalisations, but due to necessary isolation procedures did represent an estimated 12 959 person-days of lost training. 9 of 10 (90%) of sequenced isolates had a reportable lineage. All of those reported were found to be the Alpha lineage B.1.1.7.ConclusionsWe discuss the key lessons learnt from the after-action review by the Incident Management Team. These include the importance of multidisciplinary working, the utility of sync matrices to monitor outbreaks in real time, issues around Officer Cadets reporting symptoms, timing of high-risk training activities, infrastructure and use of LFDs. COVID-19 represents a vital learning opportunity to minimise the impact of potential future pandemics, which may produce considerably higher morbidity and mortality in military populations.

165. Emergence of Extensively Drug-Resistant Salmonella enterica Serotype Typhi Infections—United States, 2008–2020

Background Typhoid fever, caused by Salmonella Typhi, is fatal in 12%–30% of patients not treated with appropriate antibiotics. In 2016, a large outbreak of extensively drug-resistant (XDR) Typhi infections began in Pakistan with cases reported globally, including the United States. In 2021, the Centers for Disease Control and Prevention (CDC) issued a health advisory on XDR infections among U.S. residents without international travel. We describe resistance of Typhi infections diagnosed in the United States to help guide treatment decisions. Methods Typhoid fever is a nationally notifiable disease. Health departments report cases to CDC through the National Typhoid and Paratyphoid Fever Surveillance system. Isolates are submitted to the National Antimicrobial Resistance Monitoring System for antimicrobial susceptibility testing (AST) using broth microdilution. AST results are categorized by Clinical and Laboratory Standards Institute criteria. We defined XDR as resistant to ceftriaxone, ampicillin, chloramphenicol, and co-trimoxazole, and nonsusceptible to ciprofloxacin. Results During 2008–2019, of 4,637 Typhi isolates, 52 (1%) were ceftriaxone resistant (axo-R); 71% were ciprofloxacin nonsusceptible, 1 azithromycin resistant (azm-R), and none meropenem resistant. XDR was first detected in 2018, in 2% of 474 isolates and increased to 7% of 535 in 2019. Of the 52 axo-R isolates, 46 were XDR, of which 45 were from travelers to Pakistan, and one from a non-traveler; 6 were not XDR, of which 4 were linked to travel to Iraq. In preliminary 2020 reports, 23 isolates were XDR; 14 were from travelers to Pakistan, 8 from non-travelers, and 1 from someone with unknown travel status. Among those with XDR infection, median age was 11 years (range 1–62), 54% were female, and 62% were from 6 states. Conclusion Ceftriaxone-resistant Typhi infections, mostly XDR, are increasing. Clinicians should ask patients with suspected Typhi infections about travel and adjust treatment based on susceptibility results. Carbapenem, azithromycin, or both may be considered for empiric therapy of typhoid fever among travelers to Pakistan or Iraq and in uncommon instances when persons report no international travel. Ceftriaxone is an empiric therapy option for travelers to countries other than Pakistan and Iraq. Disclosures All Authors: No reported disclosures

Selection of Filovirus Isolates for Vaccine Development Programs

The continuing outbreaks of ebola virus disease highlight the ongoing threat posed by filoviruses. Fortunately, licensed vaccines and therapeutics are now available for Zaire ebolavirus. However, effective medical countermeasures, such as vaccines for other filoviruses such as Sudan ebolavirus and the Marburg virus, are presently in early stages of development and, in the absence of a large outbreak, would require regulatory approval via the U.S. Food and Drug Administration (FDA) Animal Rule. The selection of an appropriate animal model and virus challenge isolates for nonclinical studies are critical aspects of the development program. Here, we have focused on the recommendation of challenge isolates for Sudan ebolavirus and Marburg virus. Based on analyses led by the Filovirus Animal and Nonclinical Group (FANG) and considerations for strain selection under the FDA Guidance for the Animal Rule, we propose prototype virus isolates for use in nonclinical challenge studies.

Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka

Background: In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021.Methods: Whole genome sequencing was carried out on diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis was undertaken to further explore dominant lineages.Results: The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country until March 2021. The estimated time of the most recent common ancestor (tMRCA) of this lineage was June 1, 2020 (with 95% lower and upper bounds March 30 to July 27) suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258, as well as the more transmissible B.1.1.7 lineage, which has replaced B.1.411 to fuel the ongoing large outbreak in the country.Conclusions: The large outbreak that started in early October, is due to spread of a single virus lineage, B.1.411 until the end of March 2021, when B.1.1.7 emerged and became the dominant lineage.