Abdirahman Mahamud

Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays.

Background Many acute respiratory illness surveillance systems collect and test nasopharyngeal (NP) and/or oropharyngeal (OP) swab specimens, yet there are few studies assessing the relative measures of performance for NP versus OP specimens. Methods We collected paired NP and OP swabs separately from pediatric and adult patients with influenza-like illness or severe acute respiratory illness at two respiratory surveillance sites in Kenya. The specimens were tested for eight respiratory viruses by real-time reverse transcription-polymerase chain reaction (qRT-PCR). Positivity for a specific virus was defined as detection of viral nucleic acid in either swab. Results Of 2,331 paired NP/OP specimens, 1,402 (60.1%) were positive for at least one virus, and 393 (16.9%) were positive for more than one virus. Overall, OP swabs were significantly more sensitive than NP swabs for adenovirus (72.4% vs. 57.6%, p<0.01) and 2009 pandemic influenza A (H1N1) virus (91.2% vs. 70.4%, p<0.01). NP specimens were more sensitive for influenza B virus (83.3% vs. 61.5%, p = 0.02), parainfluenza virus 2 (85.7%, vs. 39.3%, p<0.01), and parainfluenza virus 3 (83.9% vs. 67.4%, p<0.01). The two methods did not differ significantly for human metapneumovirus, influenza A (H3N2) virus, parainfluenza virus 1, or respiratory syncytial virus. Conclusions The sensitivities were variable among the eight viruses tested; neither specimen was consistently more effective than the other. For respiratory disease surveillance programs using qRT-PCR that aim to maximize sensitivity for a large number of viruses, collecting combined NP and OP specimens would be the most effective approach.

Challenges in confirming a varicella outbreak in the two-dose vaccine era

BACKGROUND A second dose of varicella vaccine was recommended for U.S. children in 2006. We investigated a suspected varicella outbreak in School District X, Texas to determine 2-dose varicella vaccine effectiveness (VE). METHODS A varicella case was defined as an illness with maculopapulovesicular rash without other explanation with onset during April 1-June 10, 2011, in a School District X student. We conducted a retrospective cohort in the two schools with the majority of cases. Lesion, saliva, and environmental specimens were collected for varicella-zoster virus (VZV) PCR testing. VE was calculated using historic attack rates among unvaccinated. RESULTS In School District X, 82 varicella cases were reported, including 60 from Schools A and B. All cases were mild, with a median of 14 lesions. All 10 clinical specimens and 58 environmental samples tested negative for VZV. Two-dose varicella vaccination coverage was 66.4% in Schools A and B. Varicella VE in affected classrooms was 80.9% (95% CI: 67.2-88.9) among 1-dose vaccinees and 94.7% (95% CI: 89.2-97.4) among 2-dose vaccinees in School A, with a second dose incremental VE of 72.1% (95% CI: 39.0-87.3). Varicella VE among School B students did not differ significantly by dose (80.1% vs. 84.2% among 1-dose and 2-dose vaccinees, respectively). CONCLUSION Laboratory testing could not confirm varicella as the etiology of this outbreak; clinical and epidemiologic data suggests varicella as the likely cause. Better diagnostics are needed for diagnosis of varicella in vaccinated individuals so that appropriate outbreak control measures can be implemented.

Herpes Zoster-Related Deaths in the United States: Validity of Death Certificates and Mortality Rates 1979–2007

BACKGROUND Herpes zoster (HZ) vaccine was recommended in the United States to reduce HZ-associated morbidity. Vaccination may reduce HZ-associated mortality, but no strategy exists to monitor mortality trends. METHODS We validated HZ coding on death certificates from California, using hospital records as the gold standard, and applied the results to national-level data to estimate HZ mortality. RESULTS In the validation phase of the study, among 40 available hospital records listing HZ as the underlying cause of death, HZ was the underlying cause for 21 (52.5%) and a contributing cause for 5 (12.5%). Among the 21 hospital records listing HZ as the underlying cause of death, the median age of decedents was 84 years (range, 50-99); 60% had no contraindications for HZ vaccination. Of the 37 available records listing HZ as a contributing cause of death, HZ was a contributing cause for 2 (5.4%) and the underlying cause for 6 (16.2%). Nationally, in the 7 years preceding the HZ vaccination program, the average annual number of deaths in which HZ was reported as the underlying cause of death was 149; however, based on our validation study, we estimate the true number was 78 (range, 31-118). CONCLUSIONS National death certificate data greatly overestimate deaths in which HZ is the underlying or contributing cause of death. The HZ vaccination program could prevent some HZ-related deaths, but the impact will be difficult to assess using national mortality data.

Polio Outbreak Investigation and Response in Somalia, 2013

BACKGROUND For >2 decades, conflicts and recurrent natural disasters have maintained Somalia in a chronic humanitarian crisis. For nearly 5 years, 1 million children <10 years have not had access to lifesaving health services, including vaccination, resulting in the accumulation by 2012 of the largest geographically concentrated cohort of unvaccinated children in the world. This article reviews the epidemiology, risk, and program response to what is now known as the 2013 wild poliovirus (WPV) outbreak in Somalia and highlights the challenges that the program will face in making Somalia free of polio once again. METHODS A case of acute flaccid paralysis (AFP) was defined as a child <15 years of age with sudden onset of fever and paralysis. Polio cases were defined as AFP cases with stool specimens positive for WPV. RESULTS From 9 May to 31 December 2013, 189 cases of WPV type 1 (WPV1) were reported from 46 districts of Somalia; 42% were from Banadir region (Mogadishu), 60% were males, and 93% were <5 years of age. All Somalian polio cases belonged to cluster N5A, which is known to have been circulating in northern Nigeria since 2011. In response to the outbreak, 8 supplementary immunization activities were conducted with oral polio vaccine (OPV; trivalent OPV was used initially, followed subsequently by bivalent OPV) targeting various age groups, including children aged <5 years, children aged <10 years, and individuals of any age. CONCLUSIONS The current polio outbreak erupted after a polio-free period of >6 years (the last case was reported in March 2007). Somalia interrupted indigenous WPV transmission in 2002, was removed from the list of polio-endemic countries a year later, and has since demonstrated its ability to control polio outbreaks resulting from importation. This outbreak reiterates that the threat of large polio outbreaks resulting from WPV importation will remain constant unless polio transmission is interrupted in the remaining polio-endemic countries.

Risk Factors for Measles Mortality Among Hospitalized Somali Refugees Displaced by Famine, Kenya, 2011

BACKGROUND Measles among displaced, malnourished populations can result in a high case fatality ratio. In 2011, a large measles outbreak occurred in Dadaab, Kenya, among refugees fleeing famine and conflict in Somalia. The aim of this study was to identify predictors of measles deaths among hospitalized patients during the outbreak. METHODS A retrospective cohort study design was used to investigate measles mortality among hospitalized measles patients with a date of rash onset during 6 June-10 September 2011. Data were abstracted from medical records and a measles case was defined as an illness with fever, maculopapular rash, and either cough, coryza or conjunctivitis. Vaccination status was determined by patient or parental recall. Independent predictors of mortality were identified using logistic regression analysis. RESULTS Of 388 hospitalized measles patients, 188 (49%) were from hospital X, 70 (18%) from hospital Y, and 130 (34%) from hospital Z; median age was 22 years, 192 (50%) were 15-29 years of age, and 22 (6%) were vaccinated. The mean number of days from rash onset to hospitalization varied by hospital (hospital X = 5, hospital Y = 3, hospital Z = 6; P < .0001). Independent risk factors for measles mortality were neurological complications (odds ratio [OR], 12.8; 95% confidence interval [CI], 3.1-52.4), acute malnutrition (OR, 7.6; 95% CI, 1.3-44.3), and admission to hospital Z (OR, 4.2; 95% CI, 1.3-13.2). CONCLUSIONS Among Somali refugees, in addition to timely vaccination at border crossing points, early detection and treatment of acute malnutrition and proper management of measles cases may reduce measles mortality.

Measles Outbreak Response Among Adolescent and Adult Somali Refugees Displaced by Famine in Kenya and Ethiopia, 2011

BACKGROUND The refugee complexes of Dadaab, Kenya, and Dollo-Ado, Ethiopia, experienced measles outbreaks during June-November 2011, following a large influx of refugees from Somalia. METHODS Line-lists from health facilities were used to describe the outbreak in terms of age, sex, vaccination status, arrival date, attack rates (ARs), and case fatality ratios (CFRs) for each camp. Vaccination data and coverage surveys were reviewed. RESULTS In Dadaab, 1370 measles cases and 32 deaths (CFR, 2.3%) were reported. A total of 821 cases (60.1%) were aged ≥15 years, 906 (82.1%) arrived to the camps in 2011, and 1027 (79.6%) were unvaccinated. Camp-specific ARs ranged from 212 to 506 cases per 100 000 people. In Dollo-Ado, 407 cases and 23 deaths (CFR, 5.7%) were reported. Adults aged ≥15 years represented 178 cases (43.7%) and 6 deaths (26.0%). Camp-specific ARs ranged from 21 to 1100 cases per 100 000 people. Immunization activities that were part of the outbreak responses initially targeted children aged 6 months to 14 years and were later expanded to include individuals up to 30 years of age. CONCLUSIONS The target age group for outbreak response-associated immunization activities at the start of the outbreaks was inconsistent with the numbers of cases among unvaccinated adolescents and adults in the new population. In displacement of populations from areas affected by measles outbreaks, health authorities should consider vaccinating adults in routine and outbreak response activities.

Response to a Large Polio Outbreak in a Setting of Conflict — Middle East, 2013–2015

As the world advances toward the eradication of polio, outbreaks of wild poliovirus (WPV) in polio-free regions pose a substantial risk to the timeline for global eradication. Countries and regions experiencing active conflict, chronic insecurity, and large-scale displacement of persons are particularly vulnerable to outbreaks because of the disruption of health care and immunization services (1). A polio outbreak occurred in the Middle East, beginning in Syria in 2013 with subsequent spread to Iraq (2). The outbreak occurred 2 years after the onset of the Syrian civil war, resulted in 38 cases, and was the first time WPV was detected in Syria in approximately a decade (3,4). The national governments of eight countries designated the outbreak a public health emergency and collaborated with partners in the Global Polio Eradication Initiative (GPEI) to develop a multiphase outbreak response plan focused on improving the quality of acute flaccid paralysis (AFP) surveillance* and administering polio vaccines to >27 million children during multiple rounds of supplementary immunization activities (SIAs).† Successful implementation of the response plan led to containment and interruption of the outbreak within 6 months of its identification. The concerted approach adopted in response to this outbreak could serve as a model for responding to polio outbreaks in settings of conflict and political instability.

Progress Toward Polio Eradication—Somalia, 1998–2013

Since the 1988 resolution of the World Health Assembly to eradicate polio, significant progress has been made toward achieving this goal, with the result that only Afghanistan, Nigeria, and Pakistan have never successfully interrupted endemic transmission of wild poliovirus. However, one of the greatest challenges of the Global Polio Eradication Initiative has been that of maintaining the polio-free status of countries in unstable regions with weak healthcare infrastructure, a challenge exemplified by Somalia, a country in the Horn of Africa region. Somalia interrupted indigenous transmission of wild poliovirus in 2002, 4 years after the country established its national polio eradication program. But political instability and protracted armed conflict, with significant disruption of the healthcare system, have left Somalia vulnerable to 2 imported outbreaks of wild poliovirus. The first occurred during 2005-2007, resulting in >200 cases of paralytic polio, whereas the second, which began in 2013, is currently ongoing. Despite immense challenges, the country has a sensitive surveillance system that has facilitated prompt detection of outbreaks, but its weak routine immunization system means that supplementary immunization activities constitute the primary strategy for reaching children with polio vaccines. Conducting vaccination campaigns in a setting of conflict has been at times hazardous, but the countrys polio program has demonstrated resilience in overcoming many obstacles to ensure that children receive lifesaving polio vaccines. Regaining and maintaining Somalias polio-free status will depend on finding innovative and lasting solutions to the challenge of administering vaccines in a setting of ongoing conflict and instability.

Evaluation of the bag-mediated filtration system as a novel tool for poliovirus environmental surveillance: Results from a comparative field study in Pakistan

Poliovirus (PV) environmental surveillance (ES) plays an important role in the global eradication program and is crucial for monitoring silent PV circulation especially as clinical cases decrease. This study compared ES results using the novel bag-mediated filtration system (BMFS) with the current two-phase separation method. From February to November 2016, BMFS and two-phase samples were collected concurrently from twelve sites in Pakistan (n = 117). Detection was higher in BMFS than two-phase samples for each Sabin-like (SL) PV serotype (p<0.001) and wild PV type 1 (WPV1) (p = 0.065). Seventeen sampling events were positive for WPV1, with eight discordant in favor of BMFS and two in favor of two-phase. A vaccine-derived PV type 2 was detected in one BMFS sample but not the matched two-phase. After the removal of SL PV type 2 (SL2) from the oral polio vaccine in April 2016, BMFS samples detected SL2 more frequently than two-phase (p = 0.016), with the last detection by either method occurring June 12, 2016. More frequent PV detection in BMFS compared to two-phase samples is likely due to the greater effective volume assayed (1620 mL vs. 150 mL). This study demonstrated that the BMFS achieves enhanced ES for all PV serotypes in an endemic country.