Journal of Medical Virology

Genome‐wide analysis of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) strains is essential to better understand infectivity and virulence and to track coronavirus disease 2019 (COVID‐19) cases and outbreaks. We performed whole‐genome sequencing of 27 SARS‐CoV‐2 strains isolated between January 2020 and April 2020. A total of 54 mutations in different genomic regions was found. The D614G mutation, first detected in March 2020, was identified in 18 strains and was more likely associated with a lower cycle threshold (<25) in real‐time reverse‐transcription polymerase chain reaction diagnostic tests than the original D614 (prevalence ratio = 2.75; 95% confidence interval, 1.19–6.38). The integration of sequencing and epidemiological data suggests that SARS‐CoV‐2 transmission in both quarantine areas and in the community in Vietnam occur at the beginning of the epidemic although the country implemented strict quarantine quite early, with strict contact tracing, and testing. These findings provide insights into the nature of the epidemic, as well as shape strategies for COVID‐19 prevention and control in Vietnam.

We aimed to investigate the interventions of remdesivir in both diabetic and nondiabetic individuals who were suffering from a severe infection of novel coronavirus disease (COVID‐19). In this study, we aimed to explore the relationship between therapeutic effectiveness of remdesivir and complications of diabetes mellitus by observing the recovery period among diabetic and nondiabetic patients associated with COVID‐19 infection. A total of 850 COVID‐19 patients were recruited for this study, out of which 48% were diabetic and 52% were nondiabetics. The results of this study indicated that nondiabetic individuals administered with remdesivir recovered from COVID‐19 within 10 days showing a 95% confidence interval (p < 0.01), while the diabetic individuals recovered in 15 days. Nondiabetic patients administered with remdesivir exhibited higher chances of clinical improvement at 15th day than those who were associated with diabetes. Remdesivir administration improved the levels of various biochemical parameters, such as C‐reactive protein, lactate dehydrogenase, d‐Dimer, and ferritin both in diabetic and nondiabetic patients. However, a significant improvement (p < 0.01) was seen in the level of biochemical parameters among nondiabetic patients as compared to that of diabetic patients administered with remdesivir treatment. In the end, it was concluded that remdesivir could be considered as a possible therapeutic agent in the treatment of COVID‐19 both in diabetic and nondiabetic situations. However, diabetic patients showed a delayed recovery as compared with that of nondiabetic patients, in which the recovery rate was high.

Coronaviruses (CoVs) are by far the largest group of known positive‐sense RNA viruses having an extensive range of natural hosts. In the past few decades, newly evolved Coronaviruses have posed a global threat to public health. The immune response is essential to control and eliminate CoV infections, however, maladjusted immune responses may result in immunopathology and impaired pulmonary gas exchange. Gaining a deeper understanding of the interaction between Coronaviruses and the innate immune systems of the hosts may shed light on the development and persistence of inflammation in the lungs and hopefully can reduce the risk of lung inflammation caused by CoVs. In this review, we provide an update on CoV infections and relevant diseases, particularly the host defense against CoV‐induced inflammation of lung tissue, as well as the role of the innate immune system in the pathogenesis and clinical treatment.

From the end of January to mid‐June 2004 (weeks 5–24) a hepatitis A virus (HAV) outbreak occurred among a homeless and drug user community in Rotterdam, The Netherlands. To prevent further spread of the virus within this group and to the general population, the Municipal Health Service of Rotterdam organized a mass vaccination campaign during which 83% (1,515/1,800) of the homeless people were vaccinated. As part of a national HAV typing study, blood and/or fecal samples of 30 Rotterdam HAV IgM(+) patients who fell ill during the period of 1 September 2003–1 December 2004 were tested. The tests included RT‐PCR and sequencing at the VP3‐VP1 and VP1‐P2a regions of the HAV genome. It was found that 12 homeless people, one family member of a homeless person and two people without a known risk were infected with a unique subtype 3a strain. Four of the homeless patients became ill after vaccination and were probably infected at the time. This study shows that Dutch homeless people and drug users involved in HAV outbreaks should be offered HAV vaccine actively to prevent further spread of the infection. Furthermore, it was shown by molecular techniques that the unique subtype 3a strain was not found before the Rotterdam outbreak or afterwards, indicating that the mass vaccination campaign was successful. J. Med. Virol. 77:360–366, 2005. © 2005 Wiley‐Liss, Inc.

Men who have sex with men and traveling children are the most important risk groups for transmission of hepatitis A virus (HAV) in Amsterdam, The Netherlands. Between these two risk groups, different HAV genotypes are found. In this study the patterns of introduction and transmission of HAV were investigated in the two groups. HAV sequences from Amsterdam patients were divided according to risk: (I) travelers and their contacts, (II) homosexual men and their contacts. The sequences in each risk group were then grouped into clusters based on the genetic distances between the sequences. Among travelers many sporadic cases were found, the clusters were small, and introduced frequently into the population, mostly in the second half of each calendar year, indicating a seasonal pattern of introduction and transmission after the summer holidays. Among men who have sex with men the clusters were bigger and remained present for a longer time; sporadic cases were few, and introduction of new strains occurred only occasionally but throughout the year. Our findings indicate that new HAV strains are frequently imported into Amsterdam by travelers, but they are limited in the extent and season of their spread. In contrast, HAV is only occasionally imported into the male homosexual and bisexual population, but remains endemic and spreads to a large number of individuals without a seasonal pattern. J. Med. Virol. 79:488–494, 2007. © 2007 Wiley‐Liss, Inc.

The recently developed early antigen immunofluorescence (IF) method for the detection of infectious cytomegalovirus (CMV) in clinical specimens has hardly been applied on blood samples. We compared the CMV early antigen detection technique with the conventional cell culture method in 415 different buffy coat samples from 85 different immunocompromised patients. Duplicate coverslips were stained with two different monoclonal antibodies 46 days after inoculation. The conventional cultures were examined for typical cytopathic effects (CPE) during 10 weeks. Forty samples from 19 patients were positive by the IF technique, most of them with both monoclonal antibodies. Only 22 of these samples were positive in the conventional cell culture assay, on average after 15.8 days. CMV viraemia was detected exclusively by the IF method in 18 samples, 7 of which were from five patients without any further evidence of an active CMV infection. CMV viraemia was detected exclusively by the CPE method in eight samples, on average after no less than 36.6 days. CMV viraemia was not found in blood samples from 10 patients with laboratory proven active CMV infections and 53 patients without any evidence of an active CMV infection. In our hands the early antigen method for the detection of infectious CMV in blood is nearly as specific (at least 98.1%) and clearly much faster and more sensitive than the conventional cell culture method. The early CMV antigen detection method is therefore a very useful tool for the rapid detection of infectious CMV in blood.

Global rotavirus surveillance has led to the detection of many unusual human rotavirus (HRV) genotypes. During 1996–2004 surveillance within the African Rotavirus Network (ARN), six P[8],G8 and two P[6],G8 human rotavirus strains were identified. Gene fragments (RT‐PCR amplicons) of all 11‐gene segments of these G8 strains were sequenced in order to elucidate their genetic and evolutionary relationships. Phylogenetic and sequence analyses of each gene segment revealed high similarities (88–100% nt and 91–100% aa) for all segments except for gene 4 encoding VP4 proteins P[8] and P[6]. For most strains, almost all of the genes of the ARN strains other than neutralizing antigens are related to typical human strains of Wa genogroup. The VP7, NSP2, and NSP5 genes were closely related to cognate genes of animal strains (83–99% and 97–99% aa identity). This study suggests that the ARN G8 strains might have arisen through VP7 or VP4 gene reassortment events since most of the other gene segments resemble those of common human rotaviruses. However, VP7, NSP2 (likely), and NSP5 (likely) genes are derived potentially from animals consistent with a zoonotic introduction. Although these findings help elucidate rotavirus evolution, sequence studies of cognate animal rotavirus genes are needed to conclusively determine the specific origin of those genes relative to both human and animal rotavirus strains. J. Med. Virol. 81:937–951, 2009. © 2009 Wiley‐Liss, Inc.