INTRODUCTION
Over the past 2 decades, coronavirus (CoVs) have been associated with significant
disease outbreaks in East Asia and the Middle East. The severe acute respiratory
syndrome (SARS) and the Middle East respiratory syndrome (MERS) began to
emerge in 2002 and 2012, respectively. Recently, a novel coronavirus severe acute
respiratory syndrome coronavirus 2 (SARS-Co-V-2), causing coronavirus disease
2019, and it has posed a global health threat, causing an ongoing pandemic in
many countries and territories (1).
Health workers worldwide are currently making efforts to control further disease
outbreaks caused by the novel CoV (originally named 2019-nCoV), which was
first identified in Wuhan City, Hubei Province, China on 12 December 2019. On
11 February 2020, the World Health Organization (WHO) announced the official
designation for the current CoV-associated disease to be COVID-19, caused by
SARS-CoV-2. The primary cluster of patients was found to be connected with the
Huanan South China Seafood Market in Wuhan (2). CoVs belong to the family
Coronaviridae (subfamily Coronavirinae), the members of which infect a broad
trimeric SI locates itself on top of the trimeric S2 stalk (45). Recently structural
analyses of the S proteins of COVID-19 have revealed 27 amino acid substitutions
within a ,273-amino-acid stretch (16). Six substitutions are located in the RBD
(amino acids 357 to 528), while for substitutions are in the RBM at the CTD of the
SI domain (16). Of note, no amino acid change is seen in the RBM, which binds
directly to the angiotensin-converting enzymes-2 (ACE2) receptor in SARS-CoV
(16,46) At present, the main emphasis is knowing how many differences would be
required to change the host tropism. Sequence comparison revealed 17
nonsynonymous changes between the early sequence of SARS-CoV-2 and the later
isolates of SARS-CoV. The changes were found scattered over the genome of the
virus, with the nine substitutions in ORF1ab, ORF8 (4 substitutions), the spike
gene (3 substitutions), and ORF7a (single substitutions) (4). Notably, the same
nonsynonymous changes were found in a familial cluster, indicating that the viral
evolution happened during person-to-person transmission (4, 47). Such adaptive
evolution events are frequent and constitute a constantly ongoing process once the
virus spreads among new hosts (47). Even though no functional changes occur in
the virus associated with this adaptive evolution, close monitoring of the viral
absence of this protein is related to the altered virulence of coronaviruses due to
changes in morphology and tropism (54). The E protein consists of three domains,
namely, a short hydrophilic amino terminal, a large hydrophobic transmembrane
,domain, and an efficient C-terminal domain (51). The SARS-Co-V-2 E protein
reveals a similar amino acid constitution without any substitution (16).
N-Protein
The N protein of coronavirus is multipurpose. Among several functions, it
plays a role in complex formation with the viral genome, facilities M protein
interaction needed during virion assembly, and enhances the transcription
efficiency of the virus (55,56). It contains three highly conserved and distinct
domains, namely, an NTD, an RNA-biding domain or a linker region (LKR), and a
CTD (57). The NTD binds with the 3’end of the viral genome, perhaps via
electrostatic interaction, and is highly diverged both in length and sequence (58).
The charged LKR is serine and arginine rich and is also known as the SR (serine
and arginine) domain (59). The LKR is capable of direct interaction with in vitro
RNA interaction and is responsible for cell signaling (60,61). It also modulates the
antiviral response of the host by working as an antagonist for interferon.
nsps and Accessory Protein
Besides the important structural protein, the SARS-CoV-2 genome contains 15
nsps, nsp1 to nsp10 and nsp12 to nsp16, and 8 accessory proteins (3a, 3b, p6, 7a,
7b, 8b,9b, and ORF14) (16). All these proteins play a specific role in viral
replication (27). Unlike the accessory proteins of SARS-CoV, SARS-CoV-2 does
not contain 8a protein and has a longer 8b and shorter 3b protein (16). The nsp7,
nsp13, envelope, matrix, and p6 and 8b accessory proteins have not been detected
with any amino acid substitutions compared to the sequences of other
coronaviruses (16).Initially, the epicenter of the SARS-CoV-2 pandemic was
China, which reported a significant number of deaths associated with COVID-19,
with 84,458 laboratory-confirmed cases and 4,644 deaths as of 13 May 2020 (Fig.
4). As of 13 May 2020, SARS-CoV-2 confirmed cases have been reported in more
than 210 countries apart from China (Fig. 3 and 4) (WHO Situation Report 114)
(25, 64). COVID-19 has been reported on all continents expect Antarctica. For
many weeks, Italy was the focus of concerns regarding the large number of cases,
with 221,216 cases and 30911 deaths, but now, the United States is the country
with the largest number of cases, 1,322,054, and 79,634 deaths. Now, the United
Kingdom has even more cases (226,4671) and deaths (32,692) than Italy. A John
Hopkins University web platform has provided daily updates on the basic
epidemiology of the COVID-9 outbreak ship, named Diamond princess,
quarantined in Japanese water (Port of Yokohama), as well as on other cruise ships
,around the world (239) (Fig. 3). The significant events of the SARS-CoV-
/COVID-19 virus outbreak occurring since 8 December 2019 are presented as a
timeline in Fig. 5.
At the beginning, China experienced the majority of the burden associated with
COVID-19 in the form of disease morbidity and mortality (65), but over time the
COVID-19 menace moved to Europe, particularly Italy and Spain, and now the
United States has the highest number of confirmed cases another study, the average
reproductive number of COVID-19 was found to be 3.28, which is significantly
higher than the initial WHO estimate of 1.4 to 2.5(77). It is too early to obtain the
exact R0 value, since there is a possibility of bias due to insufficient data. The
higher R0 value is indicative of the more significant potential of SARS-CoV-2
transmission in a susceptible population. This is not the first time where the
culinary practices of China have been blamed for the origin of novel coronavirus
infection in human. Previously, the animals presented in the live-animal market
were identified to be the intermediate hosts of the SARS outbreak in China (78).
Several wildlife species were found to harbor potentially evolving coronavirus
strains that can overcome the species barrier (79). One of the main principles of
Chines food culture is that live-slaughtered animals are considered more nutritious
(5). After 4 months of struggle that lasted from December 2019 to March 2020, the
COVID-19 situation now seems under control in China. The wet animal markets
have reopened, and people have started buying bats, dogs, cats, birds, scorpions,
badgers, rabbits, pangolins (scaly anteaters), minks, soup from palm civet,
ostriches, hamsters, snapping turtles, ducks, fish, Siamese, crocodiles, and other as
any entry receptor while exhibiting an RBD similar to that of SARS-CoV (17, 87,
254, 255,). Several countries have provided recommendations to their people
traveling to China (88, 89). Compared to the previous coronavirus outbreaks
caused by SARS-CoV and MERS-CoV, the efficiency of SARA-CoV-2 human-to-
human transmission was thought to be less. This assumption was based on the
finding that health workers were affected less than they were in previous outbreaks
of fatal coronaviruses (2). Superspreading events are considered the main culprit
for the extensive transmission of SARS and MERS (90, 91). Almost half of the
MERS-CoV cases reported in Saudi Arabia are of secondary origin that occur
through contact with infected asymptomatic or symptomatic individuals through
human-to-human transmission (92). The occurrence of superspreading events in
the COVID-19 outbreak cannot be ruled out until its possibility is evaluated. Like
SARS and MERS, COVID-19 can also infect the lower respiratory tract, with
, milder symptoms (27). The basic reproduction number of COVID-19 has been
found to be in the range of 2.8 to 3.3 based on real time reports and 3.2 to 3.9
based on predicted infected cases (84). Route warrants the introduction of negative
fecal viral nuclei acid test results as one of the additional discharge criteria in
laboratory-confirmed cases of COVID-19 (326).
The COVID-19 pandemic does not have any novel factors, other than the
genetically unique pathogen and a further possible reservoir. The cause and the
likely future outcome are just repetitions of our previous interactions with fatal
coronaviruses. The only difference is the time of occurrence and the genetic
distinctness of pathogen involved. Mutations on the RBD of CoVs facilitated their
capability of infecting newer hosts, thereby expanding their reach to all corners of
the world (85). This is a potential threat to the health of both animals and humans.
Advanced studies using Bayesian phylogeographic reconstruction identified the
most probable origin of SARS-CoV-2 as the bat SARS-like coronavirus,
circulating in the Rhinolophus bat family (86).
Phylogenetic analysis of 10 whole-genome sequence of SARS-CoV-2 showed that
that they are related to two CoVs of bat origin, namely, bat-SL-CoVZC45 and bat-
SL-CoVZXC21, which were reported during 2018 in China (17). It was reported
that SARS-CoV-2 had been confirmed to use ACE2 as an entry receptor while
exhibiting an RBD similar fever, cough, and sputum (83). Hence, the clinicians
must be on the look-out for the possible occurrence of atypical clinical
manifestations to avoid the possibility of missed diagnosis, The early transmission
ability of SARS-CoV-2 was found to be similar to or slightly higher than that of
SARS-CoV, reflecting that it could be controlled despite moderate to high
transmissibility (84).
Increasing reports of SARS-CoV-2 in sewage and wastewater warrants the need
for further investigation due to the possibility of fecal-oral transmission. SARS-
CoV-2 present in environmental compartments such as oil and water will finally
end up in the wastewater and sewage sludge of treatment plants (328). Therefore,
we have to reevaluate the current wastewater and sewage sludge procedures and
introduce advanced techniques that are specific and effective against SARS-CoV-
2. Since there is active shedding of SARS-CoV-2 in the stool, the prevalence of
infections in a large population can be studied using wastewater-based
epidemiology. Recently, reverse transcription-quantitative PCR (RT-qPCR) was
used to enumerate the copies of SARS-CoV-2 RNA concentrated from wastewater
Over the past 2 decades, coronavirus (CoVs) have been associated with significant
disease outbreaks in East Asia and the Middle East. The severe acute respiratory
syndrome (SARS) and the Middle East respiratory syndrome (MERS) began to
emerge in 2002 and 2012, respectively. Recently, a novel coronavirus severe acute
respiratory syndrome coronavirus 2 (SARS-Co-V-2), causing coronavirus disease
2019, and it has posed a global health threat, causing an ongoing pandemic in
many countries and territories (1).
Health workers worldwide are currently making efforts to control further disease
outbreaks caused by the novel CoV (originally named 2019-nCoV), which was
first identified in Wuhan City, Hubei Province, China on 12 December 2019. On
11 February 2020, the World Health Organization (WHO) announced the official
designation for the current CoV-associated disease to be COVID-19, caused by
SARS-CoV-2. The primary cluster of patients was found to be connected with the
Huanan South China Seafood Market in Wuhan (2). CoVs belong to the family
Coronaviridae (subfamily Coronavirinae), the members of which infect a broad
trimeric SI locates itself on top of the trimeric S2 stalk (45). Recently structural
analyses of the S proteins of COVID-19 have revealed 27 amino acid substitutions
within a ,273-amino-acid stretch (16). Six substitutions are located in the RBD
(amino acids 357 to 528), while for substitutions are in the RBM at the CTD of the
SI domain (16). Of note, no amino acid change is seen in the RBM, which binds
directly to the angiotensin-converting enzymes-2 (ACE2) receptor in SARS-CoV
(16,46) At present, the main emphasis is knowing how many differences would be
required to change the host tropism. Sequence comparison revealed 17
nonsynonymous changes between the early sequence of SARS-CoV-2 and the later
isolates of SARS-CoV. The changes were found scattered over the genome of the
virus, with the nine substitutions in ORF1ab, ORF8 (4 substitutions), the spike
gene (3 substitutions), and ORF7a (single substitutions) (4). Notably, the same
nonsynonymous changes were found in a familial cluster, indicating that the viral
evolution happened during person-to-person transmission (4, 47). Such adaptive
evolution events are frequent and constitute a constantly ongoing process once the
virus spreads among new hosts (47). Even though no functional changes occur in
the virus associated with this adaptive evolution, close monitoring of the viral
absence of this protein is related to the altered virulence of coronaviruses due to
changes in morphology and tropism (54). The E protein consists of three domains,
namely, a short hydrophilic amino terminal, a large hydrophobic transmembrane
,domain, and an efficient C-terminal domain (51). The SARS-Co-V-2 E protein
reveals a similar amino acid constitution without any substitution (16).
N-Protein
The N protein of coronavirus is multipurpose. Among several functions, it
plays a role in complex formation with the viral genome, facilities M protein
interaction needed during virion assembly, and enhances the transcription
efficiency of the virus (55,56). It contains three highly conserved and distinct
domains, namely, an NTD, an RNA-biding domain or a linker region (LKR), and a
CTD (57). The NTD binds with the 3’end of the viral genome, perhaps via
electrostatic interaction, and is highly diverged both in length and sequence (58).
The charged LKR is serine and arginine rich and is also known as the SR (serine
and arginine) domain (59). The LKR is capable of direct interaction with in vitro
RNA interaction and is responsible for cell signaling (60,61). It also modulates the
antiviral response of the host by working as an antagonist for interferon.
nsps and Accessory Protein
Besides the important structural protein, the SARS-CoV-2 genome contains 15
nsps, nsp1 to nsp10 and nsp12 to nsp16, and 8 accessory proteins (3a, 3b, p6, 7a,
7b, 8b,9b, and ORF14) (16). All these proteins play a specific role in viral
replication (27). Unlike the accessory proteins of SARS-CoV, SARS-CoV-2 does
not contain 8a protein and has a longer 8b and shorter 3b protein (16). The nsp7,
nsp13, envelope, matrix, and p6 and 8b accessory proteins have not been detected
with any amino acid substitutions compared to the sequences of other
coronaviruses (16).Initially, the epicenter of the SARS-CoV-2 pandemic was
China, which reported a significant number of deaths associated with COVID-19,
with 84,458 laboratory-confirmed cases and 4,644 deaths as of 13 May 2020 (Fig.
4). As of 13 May 2020, SARS-CoV-2 confirmed cases have been reported in more
than 210 countries apart from China (Fig. 3 and 4) (WHO Situation Report 114)
(25, 64). COVID-19 has been reported on all continents expect Antarctica. For
many weeks, Italy was the focus of concerns regarding the large number of cases,
with 221,216 cases and 30911 deaths, but now, the United States is the country
with the largest number of cases, 1,322,054, and 79,634 deaths. Now, the United
Kingdom has even more cases (226,4671) and deaths (32,692) than Italy. A John
Hopkins University web platform has provided daily updates on the basic
epidemiology of the COVID-9 outbreak ship, named Diamond princess,
quarantined in Japanese water (Port of Yokohama), as well as on other cruise ships
,around the world (239) (Fig. 3). The significant events of the SARS-CoV-
/COVID-19 virus outbreak occurring since 8 December 2019 are presented as a
timeline in Fig. 5.
At the beginning, China experienced the majority of the burden associated with
COVID-19 in the form of disease morbidity and mortality (65), but over time the
COVID-19 menace moved to Europe, particularly Italy and Spain, and now the
United States has the highest number of confirmed cases another study, the average
reproductive number of COVID-19 was found to be 3.28, which is significantly
higher than the initial WHO estimate of 1.4 to 2.5(77). It is too early to obtain the
exact R0 value, since there is a possibility of bias due to insufficient data. The
higher R0 value is indicative of the more significant potential of SARS-CoV-2
transmission in a susceptible population. This is not the first time where the
culinary practices of China have been blamed for the origin of novel coronavirus
infection in human. Previously, the animals presented in the live-animal market
were identified to be the intermediate hosts of the SARS outbreak in China (78).
Several wildlife species were found to harbor potentially evolving coronavirus
strains that can overcome the species barrier (79). One of the main principles of
Chines food culture is that live-slaughtered animals are considered more nutritious
(5). After 4 months of struggle that lasted from December 2019 to March 2020, the
COVID-19 situation now seems under control in China. The wet animal markets
have reopened, and people have started buying bats, dogs, cats, birds, scorpions,
badgers, rabbits, pangolins (scaly anteaters), minks, soup from palm civet,
ostriches, hamsters, snapping turtles, ducks, fish, Siamese, crocodiles, and other as
any entry receptor while exhibiting an RBD similar to that of SARS-CoV (17, 87,
254, 255,). Several countries have provided recommendations to their people
traveling to China (88, 89). Compared to the previous coronavirus outbreaks
caused by SARS-CoV and MERS-CoV, the efficiency of SARA-CoV-2 human-to-
human transmission was thought to be less. This assumption was based on the
finding that health workers were affected less than they were in previous outbreaks
of fatal coronaviruses (2). Superspreading events are considered the main culprit
for the extensive transmission of SARS and MERS (90, 91). Almost half of the
MERS-CoV cases reported in Saudi Arabia are of secondary origin that occur
through contact with infected asymptomatic or symptomatic individuals through
human-to-human transmission (92). The occurrence of superspreading events in
the COVID-19 outbreak cannot be ruled out until its possibility is evaluated. Like
SARS and MERS, COVID-19 can also infect the lower respiratory tract, with
, milder symptoms (27). The basic reproduction number of COVID-19 has been
found to be in the range of 2.8 to 3.3 based on real time reports and 3.2 to 3.9
based on predicted infected cases (84). Route warrants the introduction of negative
fecal viral nuclei acid test results as one of the additional discharge criteria in
laboratory-confirmed cases of COVID-19 (326).
The COVID-19 pandemic does not have any novel factors, other than the
genetically unique pathogen and a further possible reservoir. The cause and the
likely future outcome are just repetitions of our previous interactions with fatal
coronaviruses. The only difference is the time of occurrence and the genetic
distinctness of pathogen involved. Mutations on the RBD of CoVs facilitated their
capability of infecting newer hosts, thereby expanding their reach to all corners of
the world (85). This is a potential threat to the health of both animals and humans.
Advanced studies using Bayesian phylogeographic reconstruction identified the
most probable origin of SARS-CoV-2 as the bat SARS-like coronavirus,
circulating in the Rhinolophus bat family (86).
Phylogenetic analysis of 10 whole-genome sequence of SARS-CoV-2 showed that
that they are related to two CoVs of bat origin, namely, bat-SL-CoVZC45 and bat-
SL-CoVZXC21, which were reported during 2018 in China (17). It was reported
that SARS-CoV-2 had been confirmed to use ACE2 as an entry receptor while
exhibiting an RBD similar fever, cough, and sputum (83). Hence, the clinicians
must be on the look-out for the possible occurrence of atypical clinical
manifestations to avoid the possibility of missed diagnosis, The early transmission
ability of SARS-CoV-2 was found to be similar to or slightly higher than that of
SARS-CoV, reflecting that it could be controlled despite moderate to high
transmissibility (84).
Increasing reports of SARS-CoV-2 in sewage and wastewater warrants the need
for further investigation due to the possibility of fecal-oral transmission. SARS-
CoV-2 present in environmental compartments such as oil and water will finally
end up in the wastewater and sewage sludge of treatment plants (328). Therefore,
we have to reevaluate the current wastewater and sewage sludge procedures and
introduce advanced techniques that are specific and effective against SARS-CoV-
2. Since there is active shedding of SARS-CoV-2 in the stool, the prevalence of
infections in a large population can be studied using wastewater-based
epidemiology. Recently, reverse transcription-quantitative PCR (RT-qPCR) was
used to enumerate the copies of SARS-CoV-2 RNA concentrated from wastewater
