病毒性肺炎常为吸入性感染,主要传染源是病人,通过飞沫和密切接触传染,可由上呼吸道病毒感染向下蔓延引起,也可继发于出疹性病毒感染,常伴气管-支气管感染.流行性感冒病毒是成年人和老人病毒性肺炎最为常见的病原,婴幼儿病毒性肺炎则常由呼吸道合胞病毒感染所致.其他如副流感病毒、巨细胞病毒、冠状病毒、腺病毒、鼻病毒和某些肠道病毒,如柯萨奇、埃可病毒等也可引起病毒性肺炎.在非细菌性肺炎中,病毒性肺炎占25%～50%,多发生于冬春季节,可散发或流行,多见于婴幼儿、老年人和原有慢性心肺疾病的病人.近年来由于免疫抑制药物广泛应用于器官移植病人,以及爱滋病发病人数的增多,病毒性肺炎的发病率逐渐增多,而SARS的流行使得病毒性肺炎显得尤为重要.一般的病毒性肺炎临床表现大多轻微,与支原体肺炎症状相似,病程1～2周.但重症肺炎可有持续高热、心悸、气急、呼吸困难、发绀,还可伴有休克和呼吸衰竭。

Viral pneumonia

Hantaviruses are a major class of zoonotic pathogens and cause a variety of severe diseases in humans. For most of the last 50 years rodents have been considered to be the primary hosts of hantaviruses, with hantavirus evolution thought to reflect a process of virus-rodent co-divergence over a time-scale of millions of years, with occasional spill-over into humans. However, recent discoveries have revealed that hantaviruses infect a more diverse range of mammalian hosts, particularly Chiroptera (bats) and Soricomorpha (moles and shrews), and that cross-species transmission at multiple scales has played an important role in hantavirus evolution. As a consequence, the evolution and emergence of hantaviruses is more complex than previously anticipated, and may serve as a realistic model for other viral groups.

The Evolution and Emergence of RNA Viruses

Acute respiratory infection (ARI) is a leading cause of mortality worldwide, of which influenza is an important cause that can be prevented with vaccination. We did a systematic review of research published from 1980 to 2009 on seasonal influenza epidemiology in sub-Saharan Africa to identify data strengths and weaknesses that might affect policy decisions, to assess the state of knowledge on influenza disease burden, and to ascertain unique features of influenza epidemiology in the region. We assessed 1203 papers, reviewed 104, and included 49 articles. 1-25% of outpatient ARI visits were caused by influenza (11 studies; mean 9·5%; median 10%), whereas 0·6-15·6% of children admitted to hospital for ARI had influenza identified (15 studies; mean 6·6%; median 6·3%). Influenza was highly seasonal in southern Africa. Other data were often absent, particularly direct measurement of influenza incidence rates for all ages, within different patient settings (outpatient, inpatient, community), and for all countries. Data from sub-Saharan Africa are insufficient to allow most countries to prioritise strategies for influenza prevention and control. Key data gaps include incidence and case-fatality ratios for all ages, the contribution of influenza towards admission of adults to hospital for ARI, representative seasonality data, economic burden, and the interaction of influenza with prevalent disorders in Africa, such as malaria, HIV, and malnutrition.

https://www.thelancet.com/pdfs/journals/laninf/PIIS1473-3099(11)70008-1.pdf

Seasonal influenza epidemiology in sub-Saharan Africa: a systematic review

Acute respiratory infections in children

Influenza infection is associated with substantial global mortality each winter season, with the greatest burden experienced in individuals aged ⩾65 years [1]. The incidence of influenza-related mortality in elderly individuals ranges from 80–150 deaths per 100,000 population for all causes and 16–22 deaths per 100,000 population for pneumonia and influenza in the United States and Europe [2–4]. Studies from high-income tropical locations, such as Hong Kong and Singapore, have found rates of excess deaths similar to those in temperate northern hemisphere countries [5, 6]. Mortality is greatest in seasons where the more severe influenza virus subtype A/H3N2 predominates, compared with the milder influenza A/H1N1 or B viruses [2].

Influenza diagnoses are generally not confirmed in the laboratory, and influenza-related deaths may be attributed to other comorbid conditions or secondary complications of infection [7]. Consequently, influenza burden estimates are generated from indirect statistical methods applied to broad disease outcomes and are quantified as the seasonal increase in mortality above a baseline of expected mortality [3, 8–10]. Seasonal increases associated with influenza virus circulation have been demonstrated for a number of mortality outcomes, including all-cause mortality, pneumonia and influenza, diabetes, cerebrovascular disease, and ischemic heart disease [3, 5, 6, 9]. By contrast, cancer deaths show no clear seasonality [9].

It has been suggested that the mortality burden associated with the 1918 influenza pandemic was greatest in low-income countries [11, 12]. Possible contributing factors include high baseline mortality rate, poor nutritional status, high prevalence of comorbid conditions, young age distribution of population, poverty, and poor access to health care [12]. While there are numerous published studies evaluating seasonal influenza-related mortality in more-affluent northern hemisphere and tropical countries [3, 4, 13], only 2 studies provide information on mortality associated with influenza in Africa, and they are geographically and temporally limited [14, 15].

Estimates of seasonal influenza mortality burden are useful to identify groups at elevated risk of mortality and to identify geographical high-risk areas. The perception that influenza does not cause substantial mortality in Africa may contribute to the underutilization of influenza vaccines, antivirals, and other control measures in this setting [16]. In addition, it is important to obtain baseline seasonal estimates of mortality burden, to allow comparison with the impact of unusual events, such as the occurrence of the novel influenza A/H1N1 2009 pandemic.

Here, we aimed to compare the influenza mortality burden between South Africa and the United States, using multiple years of data, 1998–2005, and focusing on individuals aged ⩾65 years.

Elevated Influenza-Related Excess Mortality in South African Elderly Individuals, 1998–2005

Influenza virus strains in Nairobi, Kenya.

Occult hepatitis B infection (OBI) among HIV positive patients varies widely in different geographic regions. We undertook a study to determine the prevalence of occult hepatitis B infection among HIV infected individuals visiting a health facility in South West Cameroon and characterized occult HBV strains based on sequence analyses. Plasma samples (n = 337), which previously tested negative for hepatitis B surface antigen (HBsAg), were screened for antibodies against hepatitis B core (anti-HBc) and surface (anti-HBs) antigens followed by DNA extraction. A 366 bp region covering the overlapping surface/polymerase gene of HBV was then amplified in a nested PCR and the amplicons sequenced using Sanger sequencing. The resulting sequences were then analyzed for genotypes and for escape and drug resistance mutations. Twenty samples were HBV DNA positive and were classified as OBI giving a prevalence of 5.9%. Out of these, 9 (45%) were anti-HBs positive, while 10 (52.6%) were anti-HBc positive. Additionally, 2 had dual anti-HBs and anti-HBc reactivity, while 6 had no detectable HBV antibodies. Out of the ten samples that were successfully sequenced, nine were classified as genotype E and one as genotype A. Three sequences possessed mutations associated with lamivudine resistance. We detected a number of mutations within the major hydrophilic region of the surface gene where most immune escape mutations occur. Findings from this study show the presence of hepatitis B in patients without any of the HBV serological markers. Further prospective studies are required to determine the risk factors and markers of OBI.

/pdf/characterization-of-occult-hepatitis-b-virus-infection-among-n5ywb9v544.pdf

Characterization of occult hepatitis B virus infection among HIV positive patients in Cameroon

Human herpes virus type 8 (HHV-8) is the causative agent of Kaposi's sarcoma (KS). We systematically reviewed literature published between 1998 and 2017, according to the PRISMA guidelines, to understand the distribution of HHV-8 infection in Africa. More than two-thirds (64%) of studies reported on seroprevalence and 29.3% on genotypes; 9.5% were on both seroprevalence and genotypes. About 45% of African countries had data on HHV-8 seroprevalence exclusively, and more than half (53%) had data on either seroprevalence or genotypes. Almost half (47%) of the countries had no data on HHV-8 infection. There was high heterogeneity in the types of tests and interpretation algorithms used in determining HHV-8 seropositivity across the different studies. Generally, seroprevalence ranged from 2.0% in a group of young children in Eritrea to 100% in a small group of individuals with KS in Central African Republic, and in a larger group of individuals with KS in Morocco. Approximately 16% of studies reported on children. Difference in seroprevalence across the African regions was not significant (95% CI, χ² = 0.86; p = 0.35), although specifically a relatively significant level of infection was observed in HIV-infected children. About 38% of the countries had data on K1 genotypes. K1 genotypes A, A5, B, C, F and Z occurred at frequencies of 5.3%, 26.3%, 42.1%, 18.4%, 5.3% and 2.6%, respectively. Twenty-three percent of the countries had data for K15 genotypes, and genotypes P, M and N occurred at frequencies of 52.2%, 39.1%, and 8.7%, respectively. Data on HHV-8 inter-genotype recombinants in Africa are scanty. HHV-8 may be endemic in the entire Africa continent but there is need for a harmonized testing protocol for a better understanding of HHV-8 seropositivity. K1 genotypes A5 and B, and K15 genotypes P and M, from Africa, should be considered in vaccine design efforts.

HHV-8 Seroprevalence and Genotype Distribution in Africa, 1998⁻2017: A Systematic Review.

https://ir-library.ku.ac.ke/bitstream/handle/123456789/14386/Whole%20genome%20of%20pandemic%20H1N1.....pdf;sequence=1

Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic.

We describe virus variations from patients with influenza-like illness before and after the appearance of influenza A(H1N1)pdm09 in Kenya during January 2008-July 2011. A total of 11,592 nasopharyngeal swabs were collected from consenting patients. Seasonal influenza B, A/H1N1, A/H3N2, A/H5N1, and influenza A(H1N1)pdm09 viruses were detected by real-time reverse transcription-polymerase chain reaction. Of patients enrolled, 2073 (17.9%) had influenza. A total of 1,524 (73.4%) of 2,073 samples were positive for influenza A virus and 549 (26.6%) were positive for influenza B virus. Influenza B virus predominated in 2008 and seasonal A(H1N1) virus predominated in the first half of 2009. Influenza A(H1N1)pdm09 virus predominated in the second half of 2009. Influenza A/H3N2 virus predominated in 2010, and co-circulation of influenza A(H1N1)pdm09 virus and influenza B virus predominated the first half of 2011. The reduction and displacement of seasonal A(H1N1) virus was the most obvious effect of the arrival of influenza A(H1N1)pdm09 virus. The decision of the World Health Organization to replace seasonal A(H1N1) virus with the pandemic virus strain for the southern hemisphere vaccine was appropriate for Kenya.

/pdf/impact-of-influenza-a-h1n1-pdm09-virus-on-circulation-1ca47q0jeq.pdf

George Gachara

Papers

Influenza virus strains in Nairobi, Kenya.

Characterization of occult hepatitis B virus infection among HIV positive patients in Cameroon

HHV-8 Seroprevalence and Genotype Distribution in Africa, 1998⁻2017: A Systematic Review.

Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic.

Impact of Influenza A(H1N1)pdm09 Virus on Circulation Dynamics of Seasonal Influenza Strains in Kenya