Justin Hyde

22

Title: COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing
Authors: To et al., 2020
Journal: Clinical Infectious Diseases
Date: 8/25/2020
Tags: immunity, reinfection
Reviewer: KSY
Link: https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa1275/5897019

Summary: This study intended to distinguish re-infection from prolonged viral shedding of SARS-CoV-2 using whole genome sequencing. The researchers evaluated a 33-year old male patient experiencing a second episode of infection four months (142 days) after his first symptomatic episode. The patient was asymptomatic during the second episode after returning to Hong Kong from a trip to Spain via United Kingdom. Genomic analysis was conducted on the samples from each episode to differentiate re-infection from persistent shedding. Viral genomes from the first and second episodes belonged to different clades (i.e., lineage). Viral genomes were compared using the international GISAID database to determine genomic relatives. The viral genome from the first episode was most related to strains from the United States or England collected in March and April; the second was most closely related to strains from Switzerland and England collected in July and August. This study suggests that re-infection of SARS-CoV-2 is possible with different phylogenetic strains. In this case, the second infection was milder than the previous.

Limitations: This is a report of a single individual. The role of long-term immunity is difficult to interpret from this study due to limited serological evidence during the first episode: the only sample taken during the first episode was within 10 days of onset and was negative for IgG antibodies, and antibody response may not mount until 10 or more days post-infection. This patient did develop detectable IgG after the second infection when tested at day 5 after an asymptomatic positive test.

Title: COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing
Authors: To et al., 2020
Journal: Clinical Infectious Diseases
Date: 8/25/2020
Tags: immunity, reinfection
Reviewer: KSY
Link: https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa1275/5897019

Summary: This study intended to distinguish re-infection from prolonged viral shedding of SARS-CoV-2 using whole genome sequencing. The researchers evaluated a 33-year old male patient experiencing a second episode of infection four months (142 days) after his first symptomatic episode. The patient was asymptomatic during the second episode after returning to Hong Kong from a trip to Spain via United Kingdom. Genomic analysis was conducted on the samples from each episode to differentiate re-infection from persistent shedding. Viral genomes from the first and second episodes belonged to different clades (i.e., lineage). Viral genomes were compared using the international GISAID database to determine genomic relatives. The viral genome from the first episode was most related to strains from the United States or England collected in March and April; the second was most closely related to strains from Switzerland and England collected in July and August. This study suggests that re-infection of SARS-CoV-2 is possible with different phylogenetic strains. In this case, the second infection was milder than the previous.

Limitations: This is a report of a single individual. The role of long-term immunity is difficult to interpret from this study due to limited serological evidence during the first episode: the only sample taken during the first episode was within 10 days of onset and was negative for IgG antibodies, and antibody response may not mount until 10 or more days post-infection. This patient did develop detectable IgG after the second infection when tested at day 5 after an asymptomatic positive test.

Title: Evidence that coronavirus superspreading is fat-tailed
Authors: Wong et al.,
Date: November 2, 2020
Tags: superspreading, modeling
Reviewer: KSY
Link: https://www.pnas.org/content/early/2020/10/30/2018490117

Summary: This report assessed COVID-19 superspreading events (SSEs) of SARS-CoV and SARS-CoV-2 to characterize the distribution of secondary cases resulting from an infected individual. Assuming the number of secondary cases is randomly distributed, the authors viewed SSEs as right-tail events. The authors searched previous literature on SARS-CoV and SARS-CoV-2 superspreading events with greater than six secondary cases. Data was pooled between both coronaviruses leading to a total of 45 SSEs associated with SARS-CoV-2 and 15 SSEs associated with SARS-CoV in the dataset. Using extreme value theory inferences (a method to assess the probability of an event that is more extreme than any previously observed), they observed that the distribution of secondary cases resulting from an index case to be consistent with fat-tail behavior. The tail of the distribution was not consistent with exponential decay. The authors state that this makes the distribution of secondary cases inconsistent with a negative bionomial distribution -- potentially having implication of models built under that assumption. Furthermore, they state that SSEs hmay have an outsized contribution to transmission and should be targets of interventions.

Limitations: Inclusion of SARS-CoV studies could bias the parameter estimates used in extreme value theory inferences. Because R0 is the average reproduction rate, using SSEs with greater than 6 secondary cases may not have been sufficiently high to truly evaluate the right tail of the distribution. Using a higher threshold of secondary cases in the dataset may better characterize the role of SSEs.

Title: In-Flight Transmission of SARS-CoV-2
Authors: Choi et al., 2020
Journal: Emerging Infectious Diseases
Date: September 18, 2020
Tags: Plane transmission, travel
Reviewer: KSY
Link: https://wwwnc.cdc.gov/eid/article/26/11/20-3254_article

Summary: This dispatch reports four persons diagnosed with SARS-CoV-2 who shared a flight from Boston, Massachusetts to Hong Kong, China, on March 9, 2020. This cluster was identified by examining public records of 1,110 laboratory-confirmed COVID-19 cases in Hong Kong between January 23 and June 13 for case-patients who had traveled prior to diagnosis. The flight was over 15 hours long and carried 294 passengers. Two cases were a married couple; a 58-year-old male and 61-year-old female (henceforth referred to as patient A and B). Both individuals had pre-existing conditions and developed symptoms one day after travel. Patients C and D were flight attendants. Patient C was a 25-year-old male who remained asymptomatic and was identified through contact tracing. Patient D was a 51-year-old female who developed cough and fever eight days later (March 18). All patient samples were sequenced showing the identical strain. The sequence was not consistent with samples collected in Hong Kong at the time. The viral sequence had been isolated in North America (previously found in Toronto, New York City, and Massachusetts). The authors propose that patients A and B were infected in North America and subsequently infected flight attendants (patients C and D) on the flight to Hong Kong.

Limitations: Cannot rule out the chance that patients C and D were infected prior to boarding the flight. It is possible all four patients were infected by phylogenetically matching strains of SARS-CoV-2 if they had overlapping exposures in the community.

Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens
Authors: Kim et al., 2020
Journal: JAMA
Date: 4/15/2020
Tags:
Reviewer: KSY
Link: https://jamanetwork.com/journals/jama/fullarticle/2764787

Summary: A research letter reporting co-infection rates between SARS-CoV-2 and other respiratory pathogens in northern California from March 2020. Symptomatic patients from multiple sites in northern California had nasopharyngeal swabs simultaneously tested for SARS-CoV-2 and a panel of non-SARS-CoV-2 respiratory pathogens including influenza (A/B), respiratory syncytial virus, non-SARS-CoV-2 Coronaviridae, adenovirus, parainfluenza (1-4), human metapneumovirus, rhinovirus/enterovirus, Chlamydia pneumoniae, and Mycoplasma pneumoniae. Of 1217 specimens tested for SARS-CoV-2 and other respiratory pathogens, 9.5% were positive for SARS-CoV-2 and 26.1% were positive for at least one non-SARS-CoV-2 pathogen. Of those positive for SARS-CoV-2, 20.7% (n=24) were also positive for at least one non-SARS-Cov-2 pathogen. In this sample, the most common co-infection pathogens were rhinovirus/enterovirus, respiratory syncytial virus, and non-SARS-CoV-2 coronviradae. With respect to influenza, one patient tested positive for influenza A and SARS-CoV-2.

Limitations: Sample population of the study is limited to a single region of California. Non-SARS-CoV-2 pathogens may have seasonality or spatiotemporal variations that this study may not caputure effectively considering the time of testing (i.e., spring months seasonal variation of viral epidemiology may differ from winter months). This, along with the testing guidelines and lower prevalence of SARS-CoV-2 at the time, could explain why few co-infections with influenza were observed.

SARS-CoV-2 and influenza virus co-infection
Authors: Cuadrado-Payan et al., 2020
Journal: Lancet [Correspondence]
Date: 5/5/2020
Tags: co-infection
Reviewer: KSY
Link: https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)31052-7/fulltext

Summary:
This correspondence reports four cases of SARS-CoV-2 and influenza co-infection in Spain. Three of the patients were male, ages 53 to 78 years, and the fourth was female aged 81 years. All patients were symptomatic at the time of hospitalization and tested positive for SARS-CoV-2 by RT-PCR. Two patients tested positive for influenza A, one for influenza B, and one for both A and B. All four patients had a history of hypertension. One patient was discharged after 48 hours without treatments or complications. The other three patients with past medical history of end-stage kidney disease or type-2 diabetes were admitted with and experienced rapid respiratory deterioration requiring mechanical ventilation. Treatment included lopinavir-ritonavir, hydroxychloroquine, oseltamivir, and subcutaneous interferon β-1b.

Limitations:
This is a case study observing severe co-infection among persons with pre-existing conditions and may not be applicable to the general population. Treatments used were based on available science at the time and may not be applicable for future use. From this study, quantifying severity of illness due to co-infection, comorbidities, or a combination of both cannot be discerned.